diff --git a/nats/io/client.py b/nats/io/client.py
index 34c0de0..151990c 100644
--- a/nats/io/client.py
+++ b/nats/io/client.py
@@ -392,7 +392,12 @@ def _flush_timeout(self, timeout):
     """
     future = tornado.concurrent.Future()
     yield self._send_ping(future)
-    result = yield tornado.gen.with_timeout(timedelta(seconds=timeout), future)
+    try:
+      result = yield tornado.gen.with_timeout(timedelta(seconds=timeout), future)
+    except tornado.gen.TimeoutError:
+      # Set the future to False so it can be ignored in _process_pong.
+      future.set_result(False)
+      raise
     raise tornado.gen.Return(result)
 
   @tornado.gen.coroutine
@@ -539,12 +544,17 @@ def _process_pong(self):
     The client will send a PING soon after CONNECT and then periodically
     to the server as a failure detector to close connections to unhealthy servers.
     For each PING the client sends, we will add a respective PONG future.
+    Here we want to find the oldest PONG future that is still running.  If the
+    flush PING-PONG already timed out, then just drop those old items.
     """
-    if len(self._pongs) > 0:
+    while len(self._pongs) > 0:
       future = self._pongs.pop(0)
-      future.set_result(True)
       self._pongs_received += 1
       self._pings_outstanding -= 1
+      # Only exit loop if future still running (hasn't exceeded flush timeout).
+      if future.running():
+        future.set_result(True)
+        break
 
   @tornado.gen.coroutine
   def _process_msg(self, sid, subject, reply, data):
diff --git a/tests/client_test.py b/tests/client_test.py
index 656dda7..8ec5348 100644
--- a/tests/client_test.py
+++ b/tests/client_test.py
@@ -947,6 +947,38 @@ def parse(self, data=''):
           self.assertTrue(nc.is_connected)
           self.assertFalse(nc.is_reconnecting)
 
+     @tornado.testing.gen_test
+     def test_ping_slow_replies(self):
+          pongs = []
+          class Parser():
+               def __init__(self, nc):
+                    self.nc = nc
+
+               @tornado.gen.coroutine
+               def parse(self, data=''):
+                    pongs.append(data)  # but, don't process now
+
+          nc = Client()
+          nc._ps = Parser(nc)
+          yield nc.connect(io_loop=self.io_loop,
+                           ping_interval=0.1,
+                           max_outstanding_pings=20)
+          yield tornado.gen.sleep(1)
+
+          # Should have received more than 5 pongs, but processed none.
+          self.assertTrue(len(pongs) > 5)
+          self.assertTrue(len(pongs) <= nc._pings_outstanding)
+          self.assertEqual(0, nc._pongs_received)
+          self.assertEqual(len(nc._pongs), nc._pings_outstanding)
+          # Process all that were sent.
+          expected_outstanding = nc._pings_outstanding
+          for i in range(nc._pings_outstanding):
+               yield nc._process_pong()
+               expected_outstanding -= 1
+               self.assertEqual(expected_outstanding, nc._pings_outstanding)
+               self.assertEqual(expected_outstanding, len(nc._pongs))
+               self.assertEqual(i + 1, nc._pongs_received)
+
      @tornado.testing.gen_test
      def test_flush_timeout(self):
 
@@ -969,6 +1001,35 @@ def parse(self, data=''):
           self.assertEqual(1, len(nc._pongs))
           self.assertEqual(1, nc._pings_outstanding)
 
+     @tornado.testing.gen_test
+     def test_flush_timeout_lost_message(self):
+
+          class Parser():
+               def __init__(self, nc):
+                    self.nc = nc
+                    self.drop_messages = False
+
+               @tornado.gen.coroutine
+               def parse(self, data=''):
+                    if not self.drop_messages:
+                         yield self.nc._process_pong()
+
+          nc = Client()
+          nc._ps = Parser(nc)
+          yield nc.connect(io_loop=self.io_loop)
+          nc._ps.drop_messages = True
+          with self.assertRaises(tornado.gen.TimeoutError):
+               yield nc.flush(timeout=1)
+          self.assertEqual(1, len(nc._pongs))
+          self.assertEqual(1, nc._pings_outstanding)
+          self.assertEqual(0, nc._pongs_received)
+          # Successful flush must clear timed out pong and the new one.
+          nc._ps.drop_messages = False
+          yield nc.flush(timeout=1)
+          self.assertEqual(0, len(nc._pongs))
+          self.assertEqual(0, nc._pings_outstanding)
+          self.assertEqual(2, nc._pongs_received)
+
      @tornado.testing.gen_test
      def test_timed_request_timeout(self):