diff --git a/ipykernel/inprocess/tests/test_kernel.py b/ipykernel/inprocess/tests/test_kernel.py
index 4d42e797b..c2904a006 100644
--- a/ipykernel/inprocess/tests/test_kernel.py
+++ b/ipykernel/inprocess/tests/test_kernel.py
@@ -99,6 +99,24 @@ def test_stdout(self):
         out, err = assemble_output(kc.get_iopub_msg)
         assert out == 'bar\n'
 
+    @pytest.mark.skip(
+        reason="Currently don't capture during test as pytest does its own capturing"
+    )
+    def test_capfd(self):
+        """Does correctly capture fd"""
+        kernel = InProcessKernel()
+
+        with capture_output() as io:
+            kernel.shell.run_cell('print("foo")')
+        assert io.stdout == "foo\n"
+
+        kc = BlockingInProcessKernelClient(kernel=kernel, session=kernel.session)
+        kernel.frontends.append(kc)
+        kc.execute("import os")
+        kc.execute('os.system("echo capfd")')
+        out, err = assemble_output(kc.iopub_channel)
+        assert out == "capfd\n"
+
     def test_getpass_stream(self):
         "Tests that kernel getpass accept the stream parameter"
         kernel = InProcessKernel()
diff --git a/ipykernel/iostream.py b/ipykernel/iostream.py
index ab6a2f707..0697c6ef8 100644
--- a/ipykernel/iostream.py
+++ b/ipykernel/iostream.py
@@ -12,7 +12,9 @@
 import threading
 import warnings
 from weakref import WeakSet
+import traceback
 from io import StringIO, TextIOBase
+import io
 
 import zmq
 if zmq.pyzmq_version_info() >= (17, 0):
@@ -36,6 +38,7 @@
 # IO classes
 #-----------------------------------------------------------------------------
 
+
 class IOPubThread(object):
     """An object for sending IOPub messages in a background thread
 
@@ -285,7 +288,54 @@ class OutStream(TextIOBase):
     topic = None
     encoding = 'UTF-8'
 
-    def __init__(self, session, pub_thread, name, pipe=None, echo=None):
+
+    def fileno(self):
+        """
+        Things like subprocess will peak and write to the fileno() of stderr/stdout.
+        """
+        if getattr(self, "_original_stdstream_copy", None) is not None:
+            return self._original_stdstream_copy
+        else:
+            raise io.UnsupportedOperation("fileno")
+
+    def _watch_pipe_fd(self):
+        """
+        We've redirected standards steams 0 and 1 into a pipe.
+
+        We need to watch in a thread and redirect them to the right places.
+
+        1) the ZMQ channels to show in notebook interfaces,
+        2) the original stdout/err, to capture errors in terminals.
+
+        We cannot schedule this on the ioloop thread, as this might be blocking.
+
+        """
+
+        try:
+            bts = os.read(self._fid, 1000)
+            while bts and self._should_watch:
+                self.write(bts.decode())
+                os.write(self._original_stdstream_copy, bts)
+                bts = os.read(self._fid, 1000)
+        except Exception:
+            self._exc = sys.exc_info()
+
+    def __init__(
+        self, session, pub_thread, name, pipe=None, echo=None, *, watchfd=True
+    ):
+        """
+        Parameters
+        ----------
+        name : str {'stderr', 'stdout'}
+            the name of the standard stream to replace
+        watchfd : bool (default, True)
+            Watch the file descripttor corresponding to the replaced stream.
+            This is useful if you know some underlying code will write directly
+            the file descriptor by its number. It will spawn a watching thread,
+            that will swap the give file descriptor for a pipe, read from the
+            pipe, and insert this into the current Stream.
+
+        """
         if pipe is not None:
             warnings.warn(
                 "pipe argument to OutStream is deprecated and ignored",
@@ -297,8 +347,12 @@ def __init__(self, session, pub_thread, name, pipe=None, echo=None):
         self.session = session
         if not isinstance(pub_thread, IOPubThread):
             # Backward-compat: given socket, not thread. Wrap in a thread.
-            warnings.warn("OutStream should be created with IOPubThread, not %r" % pub_thread,
-                DeprecationWarning, stacklevel=2)
+            warnings.warn(
+                "Since IPykernel 4.3, OutStream should be created with "
+                "IOPubThread, not %r" % pub_thread,
+                DeprecationWarning,
+                stacklevel=2,
+            )
             pub_thread = IOPubThread(pub_thread)
             pub_thread.start()
         self.pub_thread = pub_thread
@@ -312,12 +366,35 @@ def __init__(self, session, pub_thread, name, pipe=None, echo=None):
         self._new_buffer()
         self.echo = None
 
+        if (
+            watchfd
+            and (sys.platform.startswith("linux") or sys.platform.startswith("darwin"))
+            and ("PYTEST_CURRENT_TEST" not in os.environ)
+        ):
+            # Pytest set its own capture. Dont redirect from within pytest.
+
+            self._should_watch = True
+            self._setup_stream_redirects(name)
+
         if echo:
             if hasattr(echo, 'read') and hasattr(echo, 'write'):
                 self.echo = echo
             else:
                 raise ValueError("echo argument must be a file like object")
 
+    def _setup_stream_redirects(self, name):
+        pr, pw = os.pipe()
+        fno = getattr(sys, name).fileno()
+        self._original_stdstream_copy = os.dup(fno)
+        os.dup2(pw, fno)
+
+        self._fid = pr
+
+        self._exc = None
+        self.watch_fd_thread = threading.Thread(target=self._watch_pipe_fd)
+        self.watch_fd_thread.daemon = True
+        self.watch_fd_thread.start()
+
     def _is_master_process(self):
         return os.getpid() == self._master_pid
 
@@ -325,6 +402,12 @@ def set_parent(self, parent):
         self.parent_header = extract_header(parent)
 
     def close(self):
+        if sys.platform.startswith("linux") or sys.platform.startswith("darwin"):
+            self._should_watch = False
+            self.watch_fd_thread.join()
+        if self._exc:
+            etype, value, tb = self._exc
+            traceback.print_exception(etype, value, tb)
         self.pub_thread = None
 
     @property
diff --git a/ipykernel/kernelapp.py b/ipykernel/kernelapp.py
index ff2fdfd90..a340befe8 100644
--- a/ipykernel/kernelapp.py
+++ b/ipykernel/kernelapp.py
@@ -10,12 +10,13 @@
 import signal
 import traceback
 import logging
+from io import TextIOWrapper, FileIO
+from logging import StreamHandler
 
 import tornado
 from tornado import ioloop
 
 import zmq
-from zmq.eventloop import ioloop as zmq_ioloop
 from zmq.eventloop.zmqstream import ZMQStream
 
 from IPython.core.application import (
@@ -414,9 +415,22 @@ def init_io(self):
                                            echo=e_stdout)
             if sys.stderr is not None:
                 sys.stderr.flush()
-            sys.stderr = outstream_factory(self.session, self.iopub_thread,
-                                           'stderr',
-                                           echo=e_stderr)
+            sys.stderr = outstream_factory(
+                self.session, self.iopub_thread, "stderr", echo=e_stderr
+            )
+            if hasattr(sys.stderr, "_original_stdstream_copy"):
+
+                for handler in self.log.handlers:
+                    if isinstance(handler, StreamHandler) and (
+                        handler.stream.buffer.fileno() == 2
+                    ):
+                        self.log.debug(
+                            "Seeing logger to stderr, rerouting to raw filedescriptor."
+                        )
+
+                        handler.stream = TextIOWrapper(
+                            FileIO(sys.stderr._original_stdstream_copy, "w")
+                        )
         if self.displayhook_class:
             displayhook_factory = import_item(str(self.displayhook_class))
             self.displayhook = displayhook_factory(self.session, self.iopub_socket)
diff --git a/ipykernel/kernelbase.py b/ipykernel/kernelbase.py
index 3e99a36a5..e28baed39 100644
--- a/ipykernel/kernelbase.py
+++ b/ipykernel/kernelbase.py
@@ -231,7 +231,6 @@ def should_handle(self, stream, msg, idents):
         """
         msg_id = msg['header']['msg_id']
         if msg_id in self.aborted:
-            msg_type = msg['header']['msg_type']
             # is it safe to assume a msg_id will not be resubmitted?
             self.aborted.remove(msg_id)
             self._send_abort_reply(stream, msg, idents)
@@ -584,8 +583,7 @@ def complete_request(self, stream, ident, parent):
 
         matches = yield gen.maybe_future(self.do_complete(code, cursor_pos))
         matches = json_clean(matches)
-        completion_msg = self.session.send(stream, 'complete_reply',
-                                           matches, parent, ident)
+        self.session.send(stream, "complete_reply", matches, parent, ident)
 
     def do_complete(self, code, cursor_pos):
         """Override in subclasses to find completions.
@@ -825,9 +823,9 @@ def _send_abort_reply(self, stream, msg, idents):
         """Send a reply to an aborted request"""
         self.log.info("Aborting:")
         self.log.info("%s", msg)
-        reply_type = msg['header']['msg_type'].rsplit('_', 1)[0] + '_reply'
-        status = {'status': 'aborted'}
-        md = {'engine': self.ident}
+        reply_type = msg["header"]["msg_type"].rsplit("_", 1)[0] + "_reply"
+        status = {"status": "aborted"}
+        md = {"engine": self.ident}
         md.update(status)
         self.session.send(
             stream, reply_type, metadata=md,
diff --git a/ipykernel/tests/test_kernel.py b/ipykernel/tests/test_kernel.py
index 334748d1a..9fe09f43b 100644
--- a/ipykernel/tests/test_kernel.py
+++ b/ipykernel/tests/test_kernel.py
@@ -28,7 +28,7 @@
 def _check_master(kc, expected=True, stream="stdout"):
     execute(kc=kc, code="import sys")
     flush_channels(kc)
-    msg_id, content = execute(kc=kc, code="print (sys.%s._is_master_process())" % stream)
+    msg_id, content = execute(kc=kc, code="print(sys.%s._is_master_process())" % stream)
     stdout, stderr = assemble_output(kc.get_iopub_msg)
     assert stdout.strip() == repr(expected)
 
@@ -44,14 +44,44 @@ def _check_status(content):
 def test_simple_print():
     """simple print statement in kernel"""
     with kernel() as kc:
-        iopub = kc.iopub_channel
-        msg_id, content = execute(kc=kc, code="print ('hi')")
+        msg_id, content = execute(kc=kc, code="print('hi')")
         stdout, stderr = assemble_output(kc.get_iopub_msg)
         assert stdout == 'hi\n'
         assert stderr == ''
         _check_master(kc, expected=True)
 
 
+@pytest.mark.skip(
+    reason="Currently don't capture during test as pytest does its own capturing"
+)
+def test_capture_fd():
+    """simple print statement in kernel"""
+    with kernel() as kc:
+        iopub = kc.iopub_channel
+        msg_id, content = execute(kc=kc, code="import os; os.system('echo capsys')")
+        stdout, stderr = assemble_output(iopub)
+        assert stdout == "capsys\n"
+        assert stderr == ""
+        _check_master(kc, expected=True)
+
+
+@pytest.mark.skip(
+    reason="Currently don't capture during test as pytest does its own capturing"
+)
+def test_subprocess_peek_at_stream_fileno():
+    """"""
+    with kernel() as kc:
+        iopub = kc.iopub_channel
+        msg_id, content = execute(
+            kc=kc,
+            code="import subprocess, sys; subprocess.run(['python', '-c', 'import os; os.system(\"echo CAP1\"); print(\"CAP2\")'], stderr=sys.stderr)",
+        )
+        stdout, stderr = assemble_output(iopub)
+        assert stdout == "CAP1\nCAP2\n"
+        assert stderr == ""
+        _check_master(kc, expected=True)
+
+
 def test_sys_path():
     """test that sys.path doesn't get messed up by default"""
     with kernel() as kc:
@@ -85,7 +115,6 @@ def test_sys_path_profile_dir():
 def test_subprocess_print():
     """printing from forked mp.Process"""
     with new_kernel() as kc:
-        iopub = kc.iopub_channel
 
         _check_master(kc, expected=True)
         flush_channels(kc)
@@ -113,7 +142,6 @@ def test_subprocess_print():
 def test_subprocess_noprint():
     """mp.Process without print doesn't trigger iostream mp_mode"""
     with kernel() as kc:
-        iopub = kc.iopub_channel
 
         np = 5
         code = '\n'.join([
@@ -140,7 +168,6 @@ def test_subprocess_noprint():
 def test_subprocess_error():
     """error in mp.Process doesn't crash"""
     with new_kernel() as kc:
-        iopub = kc.iopub_channel
 
         code = '\n'.join([
             "import multiprocessing as mp",
@@ -313,8 +340,6 @@ def test_unc_paths():
         file_path = os.path.splitdrive(os.path.dirname(drive_file_path))[1]
         unc_file_path = os.path.join(unc_root, file_path[1:])
 
-        iopub = kc.iopub_channel
-
         kc.execute("cd {0:s}".format(unc_file_path))
         reply = kc.get_shell_msg(block=True, timeout=TIMEOUT)
         assert reply['content']['status'] == 'ok'