diff --git a/README.rst b/README.rst
index 8058812c..e3b6cf38 100644
--- a/README.rst
+++ b/README.rst
@@ -55,12 +55,18 @@ decoding errors. For example::
     chcp 1252
     python build.py <build commands>...
 
+In addition, some tasks within the build currently expect to be able to use
+Cygwin on Windows (https://www.cygwin.com/) to do its work. If you have
+Cygwin installed in one of the default locations (c:\cygwin or c:\cygwin64)
+then all is well. If you have it installed somewhere else then you can set
+CYGWIN_BASE in the environment and the build tool will use that for the base
+dir.
 
-If you just want to do a standard setuptools-style build using setup.py and
-are using a full source tarball, then you can stop reading at this point. If
-you want to build from a source repository checkout, or need to make changes
-and/or to regenerate some of the generated source files, then please continue
-reading.
+On the other hand, if you just want to do a standard setuptools-style build
+using setup.py and are using a full source tarball, then you can stop reading
+at this point. If you want to build from a source repository checkout, or
+need to make changes and/or to regenerate some of the generated source files,
+then please continue reading.
 
 
 Building wxWidgets
diff --git a/build.py b/build.py
index c9effa64..56309643 100755
--- a/build.py
+++ b/build.py
@@ -85,6 +85,7 @@ doxygenMD5 = {
 # And the location where they can be downloaded from
 toolsURL = 'http://wxpython.org/Phoenix/tools'
 
+
 #---------------------------------------------------------------------------
 
 def usage():
@@ -240,7 +241,7 @@ def setPythonVersion(args):
             #            
             TOOLS = os.environ.get('TOOLS')
             if 'cygdrive' in TOOLS:
-                TOOLS = runcmd('c:/cygwin/bin/cygpath -w '+TOOLS, True, False)
+                TOOLS = runcmd(getCygwinPath()+'/bin/cygpath -w '+TOOLS, True, False)
             use64flag = '--x64' in args
             if use64flag:
                 args.remove('--x64')
@@ -707,6 +708,24 @@ def getWafBuildBase():
     return base
     
         
+def getCygwinPath():
+    """
+    Try to locate the path where cygwin is installed.
+    
+    If CYGWIN_BASE is set in the environment then use that. Otherwise look in
+    default install locations.
+    """
+    if os.environ.get('CYGWIN_BASE'):
+        return os.environ.get('CYGWIN_BASE')
+    
+    for path in ['c:/cygwin', 'c:/cygwin64']:
+        if os.path.isdir(path):
+            return path
+        
+    return None
+
+    
+    
 #---------------------------------------------------------------------------
 # Command functions and helpers
 #---------------------------------------------------------------------------
@@ -717,13 +736,14 @@ def _doDox(arg):
     doxCmd = os.path.abspath(doxCmd)
     
     if isWindows:
+        cygwin_path = getCygwinPath()
         doxCmd = doxCmd.replace('\\', '/')
-        doxCmd = runcmd('c:/cygwin/bin/cygpath -u '+doxCmd, True, False)
+        doxCmd = runcmd(cygwin_path+'/bin/cygpath -u '+doxCmd, True, False)
         os.environ['DOXYGEN'] = doxCmd
         os.environ['WX_SKIP_DOXYGEN_VERSION_CHECK'] = '1'
         d = posixjoin(wxDir(), 'docs/doxygen')
         d = d.replace('\\', '/')
-        cmd = 'c:/cygwin/bin/bash.exe -l -c "cd %s && ./regen.sh %s"' % (d, arg)
+        cmd = '%s/bin/bash.exe -l -c "cd %s && ./regen.sh %s"' % (cygwin_path, d, arg)
     else:
         os.environ['DOXYGEN'] = doxCmd
         os.environ['WX_SKIP_DOXYGEN_VERSION_CHECK'] = '1'
diff --git a/sphinxtools/inheritance.py b/sphinxtools/inheritance.py
index b1dc5318..d2c970bf 100644
--- a/sphinxtools/inheritance.py
+++ b/sphinxtools/inheritance.py
@@ -269,9 +269,18 @@ class InheritanceDiagram(object):
         dot_args.extend(['-Tpng', '-o' + outfn])
         dot_args.extend(['-Tcmapx', '-o' + mapfile])
 
+        popen_args = {
+            'stdout': PIPE,
+            'stdin': PIPE,
+            'stderr': PIPE
+        }
+        
+        if sys.platform == 'win32':
+            popen_args['shell'] = True
+
         try:
 
-            p = Popen(dot_args, stdout=PIPE, stdin=PIPE, stderr=PIPE)
+            p = Popen(dot_args, **popen_args)
 
         except OSError as err: