diff --git a/cmake/FindEigency.cmake b/cmake/FindEigency.cmake
new file mode 100644
index 000000000..3e48dab64
--- /dev/null
+++ b/cmake/FindEigency.cmake
@@ -0,0 +1,27 @@
+# Find Eigency
+#
+# This code sets the following variables:
+#
+#  EIGENCY_FOUND
+#  EIGENCY_INCLUDE_DIRS
+#
+
+# Find python
+find_package( PythonInterp )
+if ( PYTHONINTERP_FOUND )
+  execute_process( COMMAND "${PYTHON_EXECUTABLE}" "-c"
+    "import eigency; includes=eigency.get_includes(include_eigen=False); print includes[0], ';', includes[1]"
+      RESULT_VARIABLE RESULT
+      OUTPUT_VARIABLE EIGENCY_INCLUDE_DIRS
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+endif ()
+
+include( FindPackageHandleStandardArgs )
+find_package_handle_standard_args(Eigency
+  FOUND_VAR
+    EIGENCY_FOUND
+  REQUIRED_VARS
+    EIGENCY_INCLUDE_DIRS
+)
+
diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 96ba18692..e0ed1eb89 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -22,22 +22,19 @@ endif()
 # extra_imports: extra header to import in the Cython pxd file.
 #                For example, to use Cython gtsam.pxd in your own module,
 #        use "from gtsam cimport *"
-# setup_py_in_path: Path to the setup.py.in config file, which will be converted
-#                   to setup.py file by cmake and used to compile the Cython module
-#                   by invoking "python setup.py build_ext --inplace"
 # install_path: destination to install the library
 # dependencies: Dependencies which need to be built before the wrapper
-function(wrap_and_install_library_cython interface_header extra_imports setup_py_in_path install_path dependencies)
+function(wrap_and_install_library_cython interface_header extra_imports install_path dependencies)
   # Paths for generated files
   get_filename_component(module_name "${interface_header}" NAME_WE)
   set(generated_files_path "${PROJECT_BINARY_DIR}/cython/${module_name}")
-  wrap_library_cython("${interface_header}" "${generated_files_path}" "${extra_imports}" "${setup_py_in_path}" "${dependencies}")
+  wrap_library_cython("${interface_header}" "${generated_files_path}" "${extra_imports}" "${dependencies}")
   install_cython_wrapped_library("${interface_header}" "${generated_files_path}" "${install_path}")
 endfunction()
 
 
 # Internal function that wraps a library and compiles the wrapper
-function(wrap_library_cython interface_header generated_files_path extra_imports setup_py_in_path dependencies)
+function(wrap_library_cython interface_header generated_files_path extra_imports dependencies)
   # Wrap codegen interface
   # Extract module path and name from interface header file name
   # wrap requires interfacePath to be *absolute*
@@ -48,34 +45,37 @@ function(wrap_library_cython interface_header generated_files_path extra_imports
   set(generated_cpp_file "${generated_files_path}/${module_name}.cpp")
 
   message(STATUS "Building wrap module ${module_name}")
-  
-  # Get build type postfix - gtsam_library_postfix is used in setup.py.in
-  # to link cythonized library to appropriate version of gtsam library
-  set(gtsam_library_postfix "")
-  if(GTSAM_BUILD_TYPE_POSTFIXES)
-    string(TOUPPER "${CMAKE_BUILD_TYPE}" build_type_upper)
-    set(gtsam_library_postfix ${CMAKE_${build_type_upper}_POSTFIX})
-  endif()
 
   # Set up generation of module source file
   file(MAKE_DIRECTORY "${generated_files_path}")
-  configure_file(${setup_py_in_path}/setup.py.in ${generated_files_path}/setup.py)
   add_custom_command(
     OUTPUT ${generated_cpp_file}
-    DEPENDS ${interface_header} wrap 
-        COMMAND 
+    DEPENDS ${interface_header} wrap
+        COMMAND
             wrap --cython
             ${module_path}
-            ${module_name} 
-            ${generated_files_path} 
+            ${module_name}
+            ${generated_files_path}
       "${extra_imports}"
-      && python setup.py build_ext --inplace
+      && cython --cplus -I. "${generated_files_path}/${module_name}.pyx"
     VERBATIM
-    WORKING_DIRECTORY ${generated_files_path})
-    
-  # Set up building of mex module
+    WORKING_DIRECTORY ${generated_files_path}/../)
   add_custom_target(${module_name}_cython_wrapper ALL DEPENDS ${generated_cpp_file} ${interface_header} ${dependencies})
-  add_custom_target(wrap_${module_name}_cython_distclean 
+
+  # Set up building of cython module
+  find_package(PythonLibs 2.7 REQUIRED)
+  include_directories(${PYTHON_INCLUDE_DIRS})
+  find_package(Eigency REQUIRED)
+  include_directories(${EIGENCY_INCLUDE_DIRS})
+
+  add_library(${module_name}_cython MODULE ${generated_cpp_file})
+  set_target_properties(${module_name}_cython PROPERTIES LINK_FLAGS "-undefined dynamic_lookup"
+    OUTPUT_NAME ${module_name} PREFIX "" LIBRARY_OUTPUT_DIRECTORY ${generated_files_path})
+  target_link_libraries(${module_name}_cython ${module_name})
+  add_dependencies(${module_name}_cython ${module_name}_cython_wrapper)
+
+  # distclean
+  add_custom_target(wrap_${module_name}_cython_distclean
       COMMAND cmake -E remove_directory ${generated_files_path})
 endfunction()
 
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index e04f29608..ea00e18d5 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -1,15 +1,30 @@
 # Install cython components
 include(GtsamCythonWrap)
-# install scripts and tests
-install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
+# Create the cython toolbox for the gtsam library
+if (GTSAM_INSTALL_CYTHON_TOOLBOX)
+  wrap_and_install_library_cython("../gtsam.h" # interface_header
+                                  ""                  # extra imports
+                                  "${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
+                                  gtsam  # dependencies which need to be built before the wrapper
+                                  )
 
-# generate __init__.py into build folder (configured with or without gtsam_unstable import line)
-# This also makes the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable
-if(GTSAM_BUILD_UNSTABLE)
-   set(GTSAM_UNSTABLE_IMPORT "from gtsam_unstable import *")
-endif()
-configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py.in ${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py)
+  # wrap gtsam_unstable
+  if(GTSAM_BUILD_UNSTABLE)
+    set(GTSAM_UNSTABLE_IMPORT "from gtsam_unstable import *")
+    wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
+                                    "from gtsam.gtsam cimport *"                  # extra imports
+                                    "${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
+                                    gtsam_unstable  # dependencies which need to be built before the wrapper
+                                    )
+    add_dependencies(gtsam_unstable_cython_wrapper gtsam_cython_wrapper)
+  endif()
 
-# Install the custom-generated __init__.py
-install_cython_files("${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py" "${GTSAM_CYTHON_INSTALL_PATH}/gtsam")
+  # Install the custom-generated __init__.py with gtsam_unstable disabled
+  # This is to make the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable
+  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py.in ${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py)
+  install_cython_files("${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py" "${GTSAM_CYTHON_INSTALL_PATH}/gtsam")
+  # install scripts and tests
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+
+endif ()
diff --git a/gtsam/CMakeLists.txt b/gtsam/CMakeLists.txt
index 8e8302ba5..ed80ff119 100644
--- a/gtsam/CMakeLists.txt
+++ b/gtsam/CMakeLists.txt
@@ -166,16 +166,3 @@ if (GTSAM_INSTALL_MATLAB_TOOLBOX)
     wrap_and_install_library(../gtsam.h "${GTSAM_ADDITIONAL_LIBRARIES}" "" "${mexFlags}")
 endif ()
 
-# Create the cython toolbox for the gtsam library
-if (GTSAM_INSTALL_CYTHON_TOOLBOX)
-    # Set up codegen
-    include(GtsamCythonWrap)
-
-    # Wrap
-    wrap_and_install_library_cython("../gtsam.h" # interface_header
-                                    ""                  # extra imports  
-                                    "../cython/gtsam"         # path to setup.py.in 
-                                    "${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
-                                    gtsam  # dependencies which need to be built before the wrapper
-                                    )
-endif ()
diff --git a/gtsam_unstable/CMakeLists.txt b/gtsam_unstable/CMakeLists.txt
index bcf53946c..448e8b00e 100644
--- a/gtsam_unstable/CMakeLists.txt
+++ b/gtsam_unstable/CMakeLists.txt
@@ -118,21 +118,6 @@ if (GTSAM_INSTALL_MATLAB_TOOLBOX)
     wrap_and_install_library(gtsam_unstable.h "gtsam" "" "${mexFlags}")
 endif(GTSAM_INSTALL_MATLAB_TOOLBOX)
 
-# Cython wrap for gtsam_unstable
-# Create the matlab toolbox for the gtsam library
-if (GTSAM_INSTALL_CYTHON_TOOLBOX)
-    # Set up codegen
-    include(GtsamCythonWrap)
-
-    # Wrap
-    wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
-                                    "from gtsam.gtsam cimport *"                  # extra imports  
-                                    "../cython/gtsam_unstable"         # path to setup.py.in 
-                                    "${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
-                                    gtsam_unstable  # dependencies which need to be built before the wrapper
-                                    )
-    add_dependencies(gtsam_unstable_cython_wrapper gtsam_cython_wrapper)
-endif ()
 
 # Build examples
 add_subdirectory(examples)