diff --git a/pre_commit_hooks/trailing_whitespace_fixer.py b/pre_commit_hooks/trailing_whitespace_fixer.py
index c159071..fa9b7dd 100644
--- a/pre_commit_hooks/trailing_whitespace_fixer.py
+++ b/pre_commit_hooks/trailing_whitespace_fixer.py
@@ -1,24 +1,27 @@
 from __future__ import print_function
 
 import argparse
-import fileinput
 import os
 import sys
 
 from pre_commit_hooks.util import cmd_output
 
 
-def _fix_file(filename, markdown=False):
-    for line in fileinput.input([filename], inplace=True):
-        # preserve trailing two-space for non-blank lines in markdown files
-        if markdown and (not line.isspace()) and (line.endswith("  \n")):
-            line = line.rstrip(' \n')
-            # only preserve if there are no trailing tabs or unusual whitespace
-            if not line[-1].isspace():
-                print(line + "  ")
-                continue
+def _fix_file(filename, is_markdown):
+    with open(filename, mode='rb') as file_processed:
+        lines = file_processed.readlines()
+    lines = [_process_line(line, is_markdown) for line in lines]
+    with open(filename, mode='wb') as file_processed:
+        for line in lines:
+            file_processed.write(line)
 
-        print(line.rstrip())
+
+def _process_line(line, is_markdown):
+    # preserve trailing two-space for non-blank lines in markdown files
+    eol = b'\r\n' if line[-2:] == b'\r\n' else b'\n'
+    if is_markdown and (not line.isspace()) and line.endswith(b'  ' + eol):
+        return line.rstrip() + b'  ' + eol
+    return line.rstrip() + eol
 
 
 def fix_trailing_whitespace(argv=None):
@@ -64,14 +67,13 @@ def fix_trailing_whitespace(argv=None):
                 .format(ext)
             )
 
-    if bad_whitespace_files:
-        for bad_whitespace_file in bad_whitespace_files:
-            print('Fixing {0}'.format(bad_whitespace_file))
-            _, extension = os.path.splitext(bad_whitespace_file.lower())
-            _fix_file(bad_whitespace_file, all_markdown or extension in md_exts)
-        return 1
-    else:
-        return 0
+    return_code = 0
+    for bad_whitespace_file in bad_whitespace_files:
+        print('Fixing {0}'.format(bad_whitespace_file))
+        _, extension = os.path.splitext(bad_whitespace_file.lower())
+        _fix_file(bad_whitespace_file, all_markdown or extension in md_exts)
+        return_code = 1
+    return return_code
 
 
 if __name__ == '__main__':

diff --git a/tests/trailing_whitespace_fixer_test.py b/tests/trailing_whitespace_fixer_test.py
index 6f4fdfd..3a72ccb 100644
--- a/tests/trailing_whitespace_fixer_test.py
+++ b/tests/trailing_whitespace_fixer_test.py
@@ -42,7 +42,7 @@ def test_fixes_trailing_markdown_whitespace(filename, input_s, output, tmpdir):
 MD_TESTS_2 = (
     ('foo.txt', 'foo  \nbar \n  \n', 'foo  \nbar\n\n'),
     ('bar.Markdown', 'bar   \nbaz\t\n\t\n', 'bar  \nbaz\n\n'),
-    ('bar.MD', 'bar   \nbaz\t   \n\t\n', 'bar  \nbaz\n\n'),
+    ('bar.MD', 'bar   \nbaz\t   \n\t\n', 'bar  \nbaz  \n\n'),
     ('.txt', 'baz   \nquux  \t\n\t\n', 'baz\nquux\n\n'),
     ('txt', 'foo   \nbaz \n\t\n', 'foo\nbaz\n\n'),
 )
@@ -103,3 +103,12 @@ def test_no_markdown_linebreak_ext_opt(filename, input_s, output, tmpdir):
 
 def test_returns_zero_for_no_changes():
     assert fix_trailing_whitespace([__file__]) == 0
+
+
+def test_preserve_non_utf8_file(tmpdir):
+    non_utf8_bytes_content = b'<a>\xe9 \n</a>\n'
+    path = tmpdir.join('file.txt')
+    path.write_binary(non_utf8_bytes_content)
+    ret = fix_trailing_whitespace([path.strpath])
+    assert ret == 1
+    assert path.size() == (len(non_utf8_bytes_content) - 1)

Non-utf8 file will cause trailing-whitespace to truncate the file contents
Hi,

(I started investigating this in https://github.com/pre-commit/pre-commit/issues/397)

Bug reproductions steps, after setting up a git repository with the "trailing-whitespace" pre-commit hook installed (with the latest sha: 775a7906cd6004bec2401a85ed16d5b3540d2f94):
```
echo -en '\x3c\x61\x3e\xe9\x20\x0a\x3c\x2f\x61\x3e' > minimal_crasher.xml
git add minimal_crasher.xml
pre-commit run trailing-whitespace --files minimal_crasher.xml
```

Results in:
````
Trim Trailing Whitespace...............................................................................................................................................................Failed
hookid: trailing-whitespace

Files were modified by this hook. Additional output:

Fixing minimal_crasher.xml
Traceback (most recent call last):
  File "/home/lucas_cimon/.pre-commit/repok3wjweh4/py_env-default/bin/trailing-whitespace-fixer", line 9, in <module>
    load_entry_point('pre-commit-hooks==0.6.0', 'console_scripts', 'trailing-whitespace-fixer')()
  File "/home/lucas_cimon/.pre-commit/repok3wjweh4/py_env-default/lib/python3.4/site-packages/pre_commit_hooks/trailing_whitespace_fixer.py", line 71, in fix_trailing_whitespace
    _fix_file(bad_whitespace_file, all_markdown or extension in md_exts)
  File "/home/lucas_cimon/.pre-commit/repok3wjweh4/py_env-default/lib/python3.4/site-packages/pre_commit_hooks/trailing_whitespace_fixer.py", line 12, in _fix_file
    for line in fileinput.input([filename], inplace=True):
  File "/usr/lib/python3.4/fileinput.py", line 263, in __next__
    line = self.readline()
  File "/usr/lib/python3.4/fileinput.py", line 363, in readline
    self._buffer = self._file.readlines(self._bufsize)
  File "/home/lucas_cimon/.pre-commit/repok3wjweh4/py_env-default/lib/python3.4/codecs.py", line 319, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 3: invalid continuation byte
```

And **all the content of `minimal_crasher.xml` lost** !!

In this test the xml file is very small, but it can happen with any file size nor number of staged modifications !

tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt[bar.MD-bar tests/trailing_whitespace_fixer_test.py::test_preserve_non_utf8_file
tests/trailing_whitespace_fixer_test.py::test_fixes_trailing_whitespace[foo tests/trailing_whitespace_fixer_test.py::test_fixes_trailing_whitespace[bar\t\nbaz\t\n-bar\nbaz\n] tests/trailing_whitespace_fixer_test.py::test_fixes_trailing_markdown_whitespace[foo.md-foo tests/trailing_whitespace_fixer_test.py::test_fixes_trailing_markdown_whitespace[bar.Markdown-bar tests/trailing_whitespace_fixer_test.py::test_fixes_trailing_markdown_whitespace[.md-baz tests/trailing_whitespace_fixer_test.py::test_fixes_trailing_markdown_whitespace[txt-foo tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt[foo.txt-foo tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt[bar.Markdown-bar tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt[.txt-baz tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt[txt-foo tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt_all[foo.baz-foo tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_opt_all[bar-bar tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_badopt[--] tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_badopt[a.b] tests/trailing_whitespace_fixer_test.py::test_markdown_linebreak_ext_badopt[a/b] tests/trailing_whitespace_fixer_test.py::test_no_markdown_linebreak_ext_opt[bar.md-bar tests/trailing_whitespace_fixer_test.py::test_no_markdown_linebreak_ext_opt[bar.markdown-baz tests/trailing_whitespace_fixer_test.py::test_returns_zero_for_no_changes