diff --git a/dvc/exceptions.py b/dvc/exceptions.py
index d5faf6268..3176bf900 100644
--- a/dvc/exceptions.py
+++ b/dvc/exceptions.py
@@ -148,3 +148,11 @@ class CyclicGraphError(DvcException):
             "{stages}".format(stages=stages)
         )
         super(CyclicGraphError, self).__init__(msg)
+
+
+class ConfirmRemoveError(DvcException):
+    def __init__(self, path):
+        super(ConfirmRemoveError, self).__init__(
+            "unable to remove '{}' without a confirmation from the user. Use "
+            "'-f' to force.".format(path)
+        )
diff --git a/dvc/prompt.py b/dvc/prompt.py
index 3d07e08b9..6853ce40b 100644
--- a/dvc/prompt.py
+++ b/dvc/prompt.py
@@ -14,7 +14,10 @@ def _ask(prompt, limited_to=None):
         return None
 
     while True:
-        answer = input(prompt + " ").lower()
+        try:
+            answer = input(prompt + " ").lower()
+        except EOFError:
+            return None
 
         if not limited_to:
             return answer
diff --git a/dvc/remote/base.py b/dvc/remote/base.py
index 6d2859c9c..ff1395c48 100644
--- a/dvc/remote/base.py
+++ b/dvc/remote/base.py
@@ -11,7 +11,7 @@ from multiprocessing import cpu_count
 import dvc.prompt as prompt
 import dvc.logger as logger
 from dvc.config import Config
-from dvc.exceptions import DvcException
+from dvc.exceptions import DvcException, ConfirmRemoveError
 
 
 STATUS_OK = 1
@@ -296,10 +296,7 @@ class RemoteBase(object):
             )
 
             if not prompt.confirm(msg):
-                raise DvcException(
-                    "unable to remove '{}' without a confirmation"
-                    " from the user. Use '-f' to force.".format(str(path_info))
-                )
+                raise ConfirmRemoveError(str(path_info))
 
         self.remove(path_info)
 
diff --git a/tests/test_checkout.py b/tests/test_checkout.py
index a1bae46ec..055287501 100644
--- a/tests/test_checkout.py
+++ b/tests/test_checkout.py
@@ -1,4 +1,5 @@
 import os
+import mock
 import yaml
 import shutil
 import filecmp
@@ -11,7 +12,7 @@ from tests.basic_env import TestDvc
 from tests.test_repro import TestRepro
 from dvc.stage import Stage
 from dvc.remote.local import RemoteLOCAL
-from dvc.exceptions import DvcException
+from dvc.exceptions import DvcException, ConfirmRemoveError
 
 from mock import patch
 
@@ -345,3 +346,21 @@ class TestCheckoutDirectory(TestRepro):
         self.assertEqual(ret, 0)
 
         self.assertTrue(os.path.exists(self.DATA_DIR))
+
+
+class TestCheckoutHook(TestDvc):
+    @mock.patch("sys.stdout.isatty", return_value=True)
+    @mock.patch("dvc.utils.compat.input", side_effect=EOFError)
+    def test(self, mock_input, mock_isatty):
+        """ Test that dvc checkout handles EOFError gracefully, which is what
+        it will experience when running in a git hook.
+        """
+        stages = self.dvc.add(self.DATA_DIR)
+        self.assertEqual(len(stages), 1)
+        stage = stages[0]
+        self.assertNotEqual(stage, None)
+
+        self.create(os.path.join(self.DATA_DIR, "test"), "test")
+
+        with self.assertRaises(ConfirmRemoveError):
+            self.dvc.checkout()
diff --git a/tests/unit/prompt.py b/tests/unit/prompt.py
new file mode 100644
index 000000000..2b6395ac7
--- /dev/null
+++ b/tests/unit/prompt.py
@@ -0,0 +1,14 @@
+import mock
+from unittest import TestCase
+
+from dvc.prompt import confirm
+
+
+class TestConfirm(TestCase):
+    @mock.patch("sys.stdout.isatty", return_value=True)
+    @mock.patch("dvc.prompt.input", side_effect=EOFError)
+    def test_eof(self, mock_input, mock_isatty):
+        ret = confirm("message")
+        mock_isatty.assert_called()
+        mock_input.assert_called()
+        self.assertFalse(ret)