diff --git a/BUILD.gn b/BUILD.gn
index cfd7227bf1..68cb2c6db7 100644
--- a/BUILD.gn
+++ b/BUILD.gn
@@ -44,24 +44,25 @@ config("deno_config") {
 }
 
 main_extern = [
+  "$rust_build:atty",
+  "$rust_build:dirs",
+  "$rust_build:futures",
+  "$rust_build:getopts",
   "$rust_build:hyper",
   "$rust_build:hyper_rustls",
-  "$rust_build:futures",
   "$rust_build:lazy_static",
   "$rust_build:libc",
   "$rust_build:log",
+  "$rust_build:rand",
+  "$rust_build:remove_dir_all",
   "$rust_build:ring",
   "$rust_build:tempfile",
-  "$rust_build:rand",
   "$rust_build:tokio",
-  "$rust_build:tokio_io",
-  "$rust_build:tokio_fs",
   "$rust_build:tokio_executor",
+  "$rust_build:tokio_fs",
+  "$rust_build:tokio_io",
   "$rust_build:tokio_threadpool",
   "$rust_build:url",
-  "$rust_build:remove_dir_all",
-  "$rust_build:dirs",
-  "$rust_build:getopts",
   "//build_extra/flatbuffers/rust:flatbuffers",
   ":msg_rs",
 ]
diff --git a/Cargo.toml b/Cargo.toml
index 3172ba3c10..96499adbd7 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -9,6 +9,7 @@ name = "deno"
 version = "0.0.0"
 
 [dependencies]
+atty = "0.2.11"
 dirs = "1.0.4"
 flatbuffers = { path = "third_party/flatbuffers/rust/flatbuffers/" }
 futures = "0.1.25"
diff --git a/build_extra/rust/BUILD.gn b/build_extra/rust/BUILD.gn
index e40a19b03d..56e0aaa96f 100644
--- a/build_extra/rust/BUILD.gn
+++ b/build_extra/rust/BUILD.gn
@@ -113,14 +113,15 @@ rust_crate("winapi") {
     "basetsd",
     "cfg",
     "cfgmgr32",
+    "consoleapi",
     "combaseapi",
     "errhandlingapi",
     "excpt",
     "fileapi",
     "guiddef",
     "handleapi",
-    "inaddr",
     "in6addr",
+    "inaddr",
     "knownfolders",
     "ktmtypes",
     "libloaderapi",
@@ -134,6 +135,7 @@ rust_crate("winapi") {
     "objbase",
     "objidl",
     "objidlbase",
+    "processenv",
     "processthreadsapi",
     "profileapi",
     "propidl",
@@ -152,8 +154,10 @@ rust_crate("winapi") {
     "vadefs",
     "vcruntime",
     "winbase",
+    "wincon",
     "wincred",
     "windef",
+    "wingdi",
     "winerror",
     "winnt",
     "winreg",
@@ -865,6 +869,14 @@ rust_crate("sct") {
   ]
 }
 
+rust_crate("atty") {
+  source_root = "$registry_github/atty-0.2.11/src/lib.rs"
+  extern = [
+    ":libc",
+    ":winapi",
+  ]
+}
+
 rust_crate("base64") {
   source_root = "$registry_github/base64-0.9.2/src/lib.rs"
   extern = [
diff --git a/src/isolate.rs b/src/isolate.rs
index e222d280fa..6530c396f5 100644
--- a/src/isolate.rs
+++ b/src/isolate.rs
@@ -6,8 +6,10 @@
 
 use deno_dir;
 use errors::DenoError;
+use errors::DenoResult;
 use flags;
 use libdeno;
+use permissions::DenoPermissions;
 use snapshot;
 
 use futures::Future;
@@ -56,6 +58,7 @@ pub struct Isolate {
 pub struct IsolateState {
   pub dir: deno_dir::DenoDir,
   pub argv: Vec<String>,
+  pub permissions: Mutex<DenoPermissions>,
   pub flags: flags::DenoFlags,
   tx: Mutex<Option<mpsc::Sender<(i32, Buf)>>>,
   pub metrics: Mutex<Metrics>,
@@ -71,6 +74,21 @@ impl IsolateState {
     tx.send((req_id, buf)).expect("tx.send error");
   }
 
+  pub fn check_write(&self, filename: &str) -> DenoResult<()> {
+    let mut perm = self.permissions.lock().unwrap();
+    perm.check_write(filename)
+  }
+
+  pub fn check_env(&self) -> DenoResult<()> {
+    let mut perm = self.permissions.lock().unwrap();
+    perm.check_env()
+  }
+
+  pub fn check_net(&self, filename: &str) -> DenoResult<()> {
+    let mut perm = self.permissions.lock().unwrap();
+    perm.check_net(filename)
+  }
+
   fn metrics_op_dispatched(
     &self,
     bytes_sent_control: u64,
@@ -143,6 +161,7 @@ impl Isolate {
       state: Arc::new(IsolateState {
         dir: deno_dir::DenoDir::new(flags.reload, custom_root).unwrap(),
         argv: argv_rest,
+        permissions: Mutex::new(DenoPermissions::new(&flags)),
         flags,
         tx: Mutex::new(Some(tx)),
         metrics: Mutex::new(Metrics::default()),
diff --git a/src/main.rs b/src/main.rs
index 91f5665230..d524b94ed5 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -31,6 +31,7 @@ mod http_util;
 mod isolate;
 mod libdeno;
 pub mod ops;
+mod permissions;
 mod resources;
 mod snapshot;
 mod tokio_util;
diff --git a/src/ops.rs b/src/ops.rs
index 37cbd68267..b7a20a46ea 100644
--- a/src/ops.rs
+++ b/src/ops.rs
@@ -1,6 +1,5 @@
 // Copyright 2018 the Deno authors. All rights reserved. MIT license.
 use errors;
-use errors::permission_denied;
 use errors::{DenoError, DenoResult, ErrorKind};
 use fs as deno_fs;
 use http_util;
@@ -333,11 +332,9 @@ fn op_set_env(
   let inner = base.inner_as_set_env().unwrap();
   let key = inner.key().unwrap();
   let value = inner.value().unwrap();
-
-  if !state.flags.allow_env {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_env() {
+    return odd_future(e);
   }
-
   std::env::set_var(key, value);
   ok_future(empty_buf())
 }
@@ -350,8 +347,8 @@ fn op_env(
   assert_eq!(data.len(), 0);
   let cmd_id = base.cmd_id();
 
-  if !state.flags.allow_env {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_env() {
+    return odd_future(e);
   }
 
   let builder = &mut FlatBufferBuilder::new();
@@ -399,8 +396,9 @@ fn op_fetch_req(
   let id = inner.id();
   let url = inner.url().unwrap();
 
-  if !state.flags.allow_net {
-    return odd_future(permission_denied());
+  // FIXME use domain (or use this inside check_net)
+  if let Err(e) = state.check_net(url) {
+    return odd_future(e);
   }
 
   let url = url.parse::<hyper::Uri>().unwrap();
@@ -513,8 +511,9 @@ fn op_make_temp_dir(
   let inner = base.inner_as_make_temp_dir().unwrap();
   let cmd_id = base.cmd_id();
 
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
+  // FIXME
+  if let Err(e) = state.check_write("make_temp") {
+    return odd_future(e);
   }
 
   let dir = inner.dir().map(PathBuf::from);
@@ -562,10 +561,9 @@ fn op_mkdir(
   let mode = inner.mode();
   let path = String::from(inner.path().unwrap());
 
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_write(&path) {
+    return odd_future(e);
   }
-
   blocking!(base.sync(), || {
     debug!("op_mkdir {}", path);
     deno_fs::mkdir(Path::new(&path), mode)?;
@@ -583,8 +581,8 @@ fn op_chmod(
   let _mode = inner.mode();
   let path = String::from(inner.path().unwrap());
 
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_write(&path) {
+    return odd_future(e);
   }
 
   blocking!(base.sync(), || {
@@ -766,11 +764,14 @@ fn op_remove(
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
   let inner = base.inner_as_remove().unwrap();
-  let path = PathBuf::from(inner.path().unwrap());
+  let path_ = inner.path().unwrap();
+  let path = PathBuf::from(path_);
   let recursive = inner.recursive();
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
+
+  if let Err(e) = state.check_write(path.to_str().unwrap()) {
+    return odd_future(e);
   }
+
   blocking!(base.sync(), || {
     debug!("op_remove {}", path.display());
     let metadata = fs::metadata(&path)?;
@@ -831,10 +832,11 @@ fn op_copy_file(
   assert_eq!(data.len(), 0);
   let inner = base.inner_as_copy_file().unwrap();
   let from = PathBuf::from(inner.from().unwrap());
-  let to = PathBuf::from(inner.to().unwrap());
+  let to_ = inner.to().unwrap();
+  let to = PathBuf::from(to_);
 
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_write(&to_) {
+    return odd_future(e);
   }
 
   debug!("op_copy_file {} {}", from.display(), to.display());
@@ -1015,14 +1017,13 @@ fn op_write_file(
   data: &'static mut [u8],
 ) -> Box<Op> {
   let inner = base.inner_as_write_file().unwrap();
-
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
-  }
-
   let filename = String::from(inner.filename().unwrap());
   let perm = inner.perm();
 
+  if let Err(e) = state.check_write(&filename) {
+    return odd_future(e);
+  }
+
   blocking!(base.sync(), || -> OpResult {
     debug!("op_write_file {} {}", filename, data.len());
     deno_fs::write_file(Path::new(&filename), data, perm)?;
@@ -1036,12 +1037,13 @@ fn op_rename(
   data: &'static mut [u8],
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
-  }
   let inner = base.inner_as_rename().unwrap();
   let oldpath = PathBuf::from(inner.oldpath().unwrap());
-  let newpath = PathBuf::from(inner.newpath().unwrap());
+  let newpath_ = inner.newpath().unwrap();
+  let newpath = PathBuf::from(newpath_);
+  if let Err(e) = state.check_write(&newpath_) {
+    return odd_future(e);
+  }
   blocking!(base.sync(), || -> OpResult {
     debug!("op_rename {} {}", oldpath.display(), newpath.display());
     fs::rename(&oldpath, &newpath)?;
@@ -1055,8 +1057,13 @@ fn op_symlink(
   data: &'static mut [u8],
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
+  let inner = base.inner_as_symlink().unwrap();
+  let oldname = PathBuf::from(inner.oldname().unwrap());
+  let newname_ = inner.newname().unwrap();
+  let newname = PathBuf::from(newname_);
+
+  if let Err(e) = state.check_write(&newname_) {
+    return odd_future(e);
   }
   // TODO Use type for Windows.
   if cfg!(windows) {
@@ -1065,10 +1072,6 @@ fn op_symlink(
       "Not implemented".to_string(),
     ));
   }
-
-  let inner = base.inner_as_symlink().unwrap();
-  let oldname = PathBuf::from(inner.oldname().unwrap());
-  let newname = PathBuf::from(inner.newname().unwrap());
   blocking!(base.sync(), || -> OpResult {
     debug!("op_symlink {} {}", oldname.display(), newname.display());
     #[cfg(any(unix))]
@@ -1118,13 +1121,14 @@ fn op_truncate(
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
 
-  if !state.flags.allow_write {
-    return odd_future(permission_denied());
-  }
-
   let inner = base.inner_as_truncate().unwrap();
   let filename = String::from(inner.name().unwrap());
   let len = inner.len();
+
+  if let Err(e) = state.check_write(&filename) {
+    return odd_future(e);
+  }
+
   blocking!(base.sync(), || {
     debug!("op_truncate {} {}", filename, len);
     let f = fs::OpenOptions::new().write(true).open(&filename)?;
@@ -1139,8 +1143,8 @@ fn op_listen(
   data: &'static mut [u8],
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
-  if !state.flags.allow_net {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_net("listen") {
+    return odd_future(e);
   }
 
   let cmd_id = base.cmd_id();
@@ -1205,10 +1209,9 @@ fn op_accept(
   data: &'static mut [u8],
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
-  if !state.flags.allow_net {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_net("accept") {
+    return odd_future(e);
   }
-
   let cmd_id = base.cmd_id();
   let inner = base.inner_as_accept().unwrap();
   let server_rid = inner.rid();
@@ -1232,10 +1235,9 @@ fn op_dial(
   data: &'static mut [u8],
 ) -> Box<Op> {
   assert_eq!(data.len(), 0);
-  if !state.flags.allow_net {
-    return odd_future(permission_denied());
+  if let Err(e) = state.check_net("dial") {
+    return odd_future(e);
   }
-
   let cmd_id = base.cmd_id();
   let inner = base.inner_as_dial().unwrap();
   let network = inner.network().unwrap();
diff --git a/src/permissions.rs b/src/permissions.rs
new file mode 100644
index 0000000000..aeeb7df9ae
--- /dev/null
+++ b/src/permissions.rs
@@ -0,0 +1,86 @@
+extern crate atty;
+
+use flags::DenoFlags;
+
+use errors::permission_denied;
+use errors::DenoResult;
+use std::io;
+
+#[derive(Debug, Default, PartialEq)]
+pub struct DenoPermissions {
+  pub allow_write: bool,
+  pub allow_net: bool,
+  pub allow_env: bool,
+}
+
+impl DenoPermissions {
+  pub fn new(flags: &DenoFlags) -> DenoPermissions {
+    DenoPermissions {
+      allow_write: flags.allow_write,
+      allow_env: flags.allow_env,
+      allow_net: flags.allow_net,
+    }
+  }
+
+  pub fn check_write(&mut self, filename: &str) -> DenoResult<()> {
+    if self.allow_write {
+      return Ok(());
+    };
+    // TODO get location (where access occurred)
+    let r = permission_prompt(format!(
+      "Deno requests write access to \"{}\".",
+      filename
+    ));;
+    if r.is_ok() {
+      self.allow_write = true;
+    }
+    r
+  }
+
+  pub fn check_net(&mut self, domain_name: &str) -> DenoResult<()> {
+    if self.allow_net {
+      return Ok(());
+    };
+    // TODO get location (where access occurred)
+    let r = permission_prompt(format!(
+      "Deno requests network access to \"{}\".",
+      domain_name
+    ));
+    if r.is_ok() {
+      self.allow_net = true;
+    }
+    r
+  }
+
+  pub fn check_env(&mut self) -> DenoResult<()> {
+    if self.allow_env {
+      return Ok(());
+    };
+    // TODO get location (where access occurred)
+    let r = permission_prompt(
+      "Deno requests access to environment variables.".to_string(),
+    );
+    if r.is_ok() {
+      self.allow_env = true;
+    }
+    r
+  }
+}
+
+fn permission_prompt(message: String) -> DenoResult<()> {
+  if !atty::is(atty::Stream::Stdin) || !atty::is(atty::Stream::Stderr) {
+    return Err(permission_denied());
+  };
+  // print to stderr so that if deno is > to a file this is still displayed.
+  eprint!("{} Grant? [yN] ", message);
+  let mut input = String::new();
+  let stdin = io::stdin();
+  let _nread = stdin.read_line(&mut input)?;
+  let ch = input.chars().next().unwrap();
+  let is_yes = ch == 'y' || ch == 'Y';
+  if is_yes {
+    Ok(())
+  } else {
+    Err(permission_denied())
+  }
+}
diff --git a/third_party b/third_party
index b93f9c8bd3..56c4acce2e 160000
--- a/third_party
+++ b/third_party
@@ -1 +1 @@
-Subproject commit b93f9c8bd39a2548d60167043da6b947c023a830
+Subproject commit 56c4acce2e8ffe979b2e7d52d2b3e6f613ed492e
diff --git a/tools/permission_prompt_test.py b/tools/permission_prompt_test.py
new file mode 100755
index 0000000000..2bc24d12ca
--- /dev/null
+++ b/tools/permission_prompt_test.py
@@ -0,0 +1,143 @@
+#!/usr/bin/env python
+import os
+import pty
+import select
+import subprocess
+
+from util import build_path, executable_suffix
+
+PERMISSIONS_PROMPT_TEST_TS = "tools/permission_prompt_test.ts"
+
+
+# This function is copied from:
+# https://gist.github.com/hayd/4f46a68fc697ba8888a7b517a414583e
+# https://stackoverflow.com/q/52954248/1240268
+def tty_capture(cmd, bytes_input):
+    """Capture the output of cmd with bytes_input to stdin,
+    with stdin, stdout and stderr as TTYs."""
+    mo, so = pty.openpty()  # provide tty to enable line-buffering
+    me, se = pty.openpty()
+    mi, si = pty.openpty()
+    fdmap = {mo: 'stdout', me: 'stderr', mi: 'stdin'}
+
+    p = subprocess.Popen(
+        cmd, bufsize=1, stdin=si, stdout=so, stderr=se, close_fds=True)
+    os.write(mi, bytes_input)
+
+    timeout = .04  # seconds
+    res = {'stdout': b'', 'stderr': b''}
+    while True:
+        ready, _, _ = select.select([mo, me], [], [], timeout)
+        if ready:
+            for fd in ready:
+                data = os.read(fd, 512)
+                if not data:
+                    break
+                res[fdmap[fd]] += data
+        elif p.poll() is not None:  # select timed-out
+            break  # p exited
+    for fd in [si, so, se, mi, mo, me]:
+        os.close(fd)  # can't do it sooner: it leads to errno.EIO error
+    p.wait()
+    return p.returncode, res['stdout'], res['stderr']
+
+
+class Prompt(object):
+    def __init__(self, deno_exe):
+        self.deno_exe = deno_exe
+
+    def run(self,
+            arg,
+            bytes_input,
+            allow_write=False,
+            allow_net=False,
+            allow_env=False):
+        "Returns (return_code, stdout, stderr)."
+        cmd = [self.deno_exe, PERMISSIONS_PROMPT_TEST_TS, arg]
+        if allow_write:
+            cmd.append("--allow-write")
+        if allow_net:
+            cmd.append("--allow-net")
+        if allow_env:
+            cmd.append("--allow-env")
+        return tty_capture(cmd, bytes_input)
+
+    def warm_up(self):
+        # ignore the ts compiling message
+        self.run('needsWrite', b'', allow_write=True)
+
+    def test_write_yes(self):
+        code, stdout, stderr = self.run('needsWrite', b'y\n')
+        assert code == 0
+        assert stdout == b''
+        assert b'Deno requests write access' in stderr
+
+    def test_write_arg(self):
+        code, stdout, stderr = self.run('needsWrite', b'', allow_write=True)
+        assert code == 0
+        assert stdout == b''
+        assert stderr == b''
+
+    def test_write_no(self):
+        code, stdout, stderr = self.run('needsWrite', b'N\n')
+        assert code == 1
+        # FIXME this error message should be in stderr
+        assert b'PermissionDenied: permission denied' in stdout
+        assert b'Deno requests write access' in stderr
+
+    def test_env_yes(self):
+        code, stdout, stderr = self.run('needsEnv', b'y\n')
+        assert code == 0
+        assert stdout == b''
+        assert b'Deno requests access to environment' in stderr
+
+    def test_env_arg(self):
+        code, stdout, stderr = self.run('needsEnv', b'', allow_env=True)
+        assert code == 0
+        assert stdout == b''
+        assert stderr == b''
+
+    def test_env_no(self):
+        code, stdout, stderr = self.run('needsEnv', b'N\n')
+        assert code == 1
+        # FIXME this error message should be in stderr
+        assert b'PermissionDenied: permission denied' in stdout
+        assert b'Deno requests access to environment' in stderr
+
+    def test_net_yes(self):
+        code, stdout, stderr = self.run('needsEnv', b'y\n')
+        assert code == 0
+        assert stdout == b''
+        assert b'Deno requests access to environment' in stderr
+
+    def test_net_arg(self):
+        code, stdout, stderr = self.run('needsNet', b'', allow_net=True)
+        assert code == 0
+        assert stdout == b''
+        assert stderr == b''
+
+    def test_net_no(self):
+        code, stdout, stderr = self.run('needsNet', b'N\n')
+        assert code == 1
+        # FIXME this error message should be in stderr
+        assert b'PermissionDenied: permission denied' in stdout
+        assert b'Deno requests network access' in stderr
+
+
+def permission_prompt_test(deno_exe):
+    p = Prompt(deno_exe)
+    p.warm_up()
+    p.test_write_yes()
+    p.test_write_arg()
+    p.test_write_no()
+    p.test_env_yes()
+    p.test_env_arg()
+    p.test_env_no()
+    p.test_net_yes()
+    p.test_net_arg()
+    p.test_net_no()
+
+
+if __name__ == "__main__":
+    deno_exe = os.path.join(build_path(), "deno" + executable_suffix)
+    permission_prompt_test(deno_exe)
diff --git a/tools/permission_prompt_test.ts b/tools/permission_prompt_test.ts
new file mode 100644
index 0000000000..cf8a09805c
--- /dev/null
+++ b/tools/permission_prompt_test.ts
@@ -0,0 +1,21 @@
+import { args, listen, env, exit, makeTempDirSync } from "deno";
+
+const name = args[1];
+const test = {
+  needsWrite: () => {
+    makeTempDirSync();
+  },
+  needsEnv: () => {
+    env().home;
+  },
+  needsNet: () => {
+    listen("tcp", "127.0.0.1:4540");
+  }
+}[name];
+
+if (!test) {
+  console.log("Unknown test:", name);
+  exit(1);
+}
+
+test();
diff --git a/tools/test.py b/tools/test.py
index fb05442564..e2d0772453 100755
--- a/tools/test.py
+++ b/tools/test.py
@@ -60,6 +60,13 @@ def main(argv):
 
     check_output_test(deno_exe)
 
+    # TODO We currently skip testing the prompt in Windows completely.
+    # Windows does not support the pty module used for testing the permission
+    # prompt.
+    if os.name != 'nt':
+        from permission_prompt_test import permission_prompt_test
+        permission_prompt_test(deno_exe)
+
     rmtree(deno_dir)
 
     deno_dir_test(deno_exe, deno_dir)
diff --git a/tools/third_party.py b/tools/third_party.py
index d6c97f13b9..65ff437b79 100644
--- a/tools/third_party.py
+++ b/tools/third_party.py
@@ -125,8 +125,8 @@ def run_cargo():
     # If the lockfile ends up in the git repo, it'll make cargo hang for everyone
     # else who tries to run sync_third_party.
     def delete_lockfile():
-        lockfiles = find_exts(
-            path.join(rust_crates_path, "registry/index"), '.cargo-index-lock')
+        lockfiles = find_exts([path.join(rust_crates_path, "registry/index")],
+                              ['.cargo-index-lock'])
         for lockfile in lockfiles:
             os.remove(lockfile)