diff --git a/wrap/Class.cpp b/wrap/Class.cpp
index 20c4084e0..1fda16ef6 100644
--- a/wrap/Class.cpp
+++ b/wrap/Class.cpp
@@ -672,8 +672,8 @@ void Class::python_wrapper(FileWriter& wrapperFile) const {
 }
 
 /* ************************************************************************* */
-void Class::cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile) const {
-  string cythonClassName = qualifiedName("_");
+void Class::emit_cython_pxd(FileWriter& pxdFile) const {
+  string cythonClassName = qualifiedName("_", 1);
   pxdFile.oss << "cdef extern from \"" << includeFile << "\" namespace \""
                 << qualifiedNamespaces("::") << "\":" << endl;
   pxdFile.oss << "\tcdef cppclass " << cythonClassName << " \"" << qualifiedName("::") << "\"";
@@ -688,13 +688,7 @@ void Class::cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile) const {
   if (parentClass) pxdFile.oss << "(" <<  parentClass->qualifiedName("_") << ")";
   pxdFile.oss << ":\n";
 
-  pyxFile.oss << "cdef class " << name();
-  if (parentClass) pyxFile.oss << "(" <<  parentClass->name() << ")";
-  pyxFile.oss << ":\n";
-  pyxFile.oss << "\tcdef shared_ptr[" << cythonClassName << "] "
-              << "gt" << name() << "_\n";
-
-  constructor.cython_wrapper(pxdFile, pyxFile, cythonClassName);
+  constructor.emit_cython_pxd(pxdFile, cythonClassName);
   if (constructor.nrOverloads()>0) pxdFile.oss << "\n";
 
   for(const StaticMethod& m: static_methods | boost::adaptors::map_values)
@@ -710,6 +704,17 @@ void Class::cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile) const {
   if (numMethods == 0)
       pxdFile.oss << "\t\tpass";
   pxdFile.oss << "\n\n";  
+}
+
+void Class::emit_cython_pyx(FileWriter& pyxFile) const {
+  string cythonClassName = qualifiedName("_", 1);
+  pyxFile.oss << "cdef class " << name();
+  if (parentClass) pyxFile.oss << "(" <<  parentClass->name() << ")";
+  pyxFile.oss << ":\n";
+  pyxFile.oss << "\tcdef shared_ptr[" << cythonClassName << "] "
+              << "gt" << name() << "_\n";
+
+  constructor.emit_cython_pyx(pyxFile, cythonClassName);
 
   pyxFile.oss << "\n";
 }
diff --git a/wrap/Class.h b/wrap/Class.h
index ad9fec9e9..c9b80ba30 100644
--- a/wrap/Class.h
+++ b/wrap/Class.h
@@ -148,7 +148,8 @@ public:
   void python_wrapper(FileWriter& wrapperFile) const;
 
   // emit cython wrapper
-  void cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile) const;
+  void emit_cython_pxd(FileWriter& pxdFile) const;
+  void emit_cython_pyx(FileWriter& pyxFile) const;
 
   friend std::ostream& operator<<(std::ostream& os, const Class& cls) {
     os << "class " << cls.name() << "{\n";
diff --git a/wrap/Constructor.cpp b/wrap/Constructor.cpp
index a15197813..fce4a25d6 100644
--- a/wrap/Constructor.cpp
+++ b/wrap/Constructor.cpp
@@ -121,7 +121,7 @@ void Constructor::python_wrapper(FileWriter& wrapperFile, Str className) const {
 }
 
 /* ************************************************************************* */
-void Constructor::cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile, Str className) const {
+void Constructor::emit_cython_pxd(FileWriter& pxdFile, Str className) const {
   for (size_t i = 0; i < nrOverloads(); i++) {
     ArgumentList args = argumentList(i);
     pxdFile.oss << "\t\t" << className << "(";
@@ -131,3 +131,7 @@ void Constructor::cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile, Str c
 }
 
 /* ************************************************************************* */
+void Constructor::emit_cython_pyx(FileWriter& pyxFile, Str className) const {
+}
+
+/* ************************************************************************* */
diff --git a/wrap/Constructor.h b/wrap/Constructor.h
index ed55715b8..ace630c4b 100644
--- a/wrap/Constructor.h
+++ b/wrap/Constructor.h
@@ -79,7 +79,8 @@ struct Constructor: public OverloadedFunction {
   void python_wrapper(FileWriter& wrapperFile, Str className) const;
 
   // emit cython wrapper
-  void cython_wrapper(FileWriter& pxdFile, FileWriter& pyxFile, Str className) const;
+  void emit_cython_pxd(FileWriter& pxdFile, Str className) const;
+  void emit_cython_pyx(FileWriter& pyxFile, Str className) const;
 
   friend std::ostream& operator<<(std::ostream& os, const Constructor& m) {
     for (size_t i = 0; i < m.nrOverloads(); i++)
diff --git a/wrap/Module.cpp b/wrap/Module.cpp
index 1036ee8ca..e7e4ec819 100644
--- a/wrap/Module.cpp
+++ b/wrap/Module.cpp
@@ -294,13 +294,16 @@ void Module::cython_code(const string& toolboxPath) const {
   FileWriter pxdFile(pxdFileName, verbose, "#");
   FileWriter pyxFile(pyxFileName, verbose, "#");
 
-  // create proxy class and wrapper code
+  // create cython pxd file
   for(const Class& cls: uninstantiatedClasses)
-    cls.cython_wrapper(pxdFile, pyxFile);
-
+    cls.emit_cython_pxd(pxdFile);
   // finish wrapper file
   pxdFile.oss << "\n";
   pxdFile.emit(true);
+
+  // create cython pyx file
+  for(const Class& cls: uninstantiatedClasses)
+    cls.emit_cython_pyx(pyxFile);
   pyxFile.oss << "\n";
   pyxFile.emit(true);
 }
diff --git a/wrap/Qualified.h b/wrap/Qualified.h
index 31148ebe6..52bf19914 100644
--- a/wrap/Qualified.h
+++ b/wrap/Qualified.h
@@ -137,9 +137,9 @@ public:
   }
 
   /// Return a qualified string using given delimiter
-  std::string qualifiedName(const std::string& delimiter = "") const {
+  std::string qualifiedName(const std::string& delimiter = "", size_t fromLevel = 0) const {
     std::string result;
-    for (std::size_t i = 0; i < namespaces_.size(); ++i)
+    for (std::size_t i = fromLevel; i < namespaces_.size(); ++i)
       result += (namespaces_[i] + delimiter);
     result += name_;
     return result;