diff --git a/pycodestyle.py b/pycodestyle.py
index deb45395..88eb4d75 100755
--- a/pycodestyle.py
+++ b/pycodestyle.py
@@ -264,7 +264,7 @@ def trailing_blank_lines(physical_line, lines, line_number, total_lines):
     However the last line should end with a new line (warning W292).
     """
     if line_number == total_lines:
-        stripped_last_line = physical_line.rstrip()
+        stripped_last_line = physical_line.rstrip('\r\n')
         if physical_line and not stripped_last_line:
             return 0, "W391 blank line at end of file"
         if stripped_last_line == physical_line:
@@ -2125,21 +2125,30 @@ def generate_tokens(self):
             self.report_error(1, 0, 'E902 %s' % self._io_error, readlines)
         tokengen = tokenize.generate_tokens(self.readline)
         try:
+            prev_physical = ''
             for token in tokengen:
                 if token[2][0] > self.total_lines:
                     return
                 self.noqa = token[4] and noqa(token[4])
-                self.maybe_check_physical(token)
+                self.maybe_check_physical(token, prev_physical)
                 yield token
+                prev_physical = token[4]
         except (SyntaxError, tokenize.TokenError):
             self.report_invalid_syntax()
 
-    def maybe_check_physical(self, token):
+    def maybe_check_physical(self, token, prev_physical):
         """If appropriate for token, check current physical line(s)."""
         # Called after every token, but act only on end of line.
+
+        # a newline token ends a single physical line.
         if _is_eol_token(token):
-            # Obviously, a newline token ends a single physical line.
-            self.check_physical(token[4])
+            # if the file does not end with a newline, the NEWLINE
+            # token is inserted by the parser, but it does not contain
+            # the previous physical line in `token[4]`
+            if token[4] == '':
+                self.check_physical(prev_physical)
+            else:
+                self.check_physical(token[4])
         elif token[0] == tokenize.STRING and '\n' in token[1]:
             # Less obviously, a string that contains newlines is a
             # multiline string, either triple-quoted or with internal
diff --git a/testsuite/W29.py b/testsuite/W29.py
index 4050c2ff..e9ad5800 100644
--- a/testsuite/W29.py
+++ b/testsuite/W29.py
@@ -9,6 +9,11 @@ class Foo(object):
 #: W291:2:35
 '''multiline
 string with trailing whitespace'''   
+#: W291 W292 noeol
+x = 1   
+#: W191 W292 noeol
+if False:
+	pass  # indented with tabs
 #: W292:1:36 noeol
 # This line doesn't have a linefeed
 #: W292:1:5 E225:1:2 noeol
diff --git a/testsuite/W39.py b/testsuite/W39.py
index 68f886be..25e05b05 100644
--- a/testsuite/W39.py
+++ b/testsuite/W39.py
@@ -5,7 +5,7 @@
 # Two additional empty lines
 
 
-#: W391:4:1 W293:3:1 W293:4:1 noeol
+#: W292:4:5 W293:3:1 W293:4:1 noeol
 # The last lines contain space