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 "${PYTHON_EXECUTABLE}" "-c"
+    "import eigency; includes=eigency.get_includes(include_eigen=False); print includes[0], ';', includes[1]"
+      RESULT_VARIABLE RESULT
+      OUTPUT_VARIABLE EIGENCY_INCLUDE_DIRS
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+endif ()
+
+include( FindPackageHandleStandardArgs )
+find_package_handle_standard_args(Eigency
+  FOUND_VAR
+    EIGENCY_FOUND
+  REQUIRED_VARS
+    EIGENCY_INCLUDE_DIRS
+)
+
diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 291b6a22a..e0ed1eb89 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -11,32 +11,30 @@ if(NOT GTSAM_CYTHON_INSTALL_PATH)
   set(GTSAM_CYTHON_INSTALL_PATH "${CMAKE_INSTALL_PREFIX}/cython")
 endif()
 
-# User-friendly Cython wrapping and installing function.  
-# Builds a Cython module from the provided interface_header.  
+# User-friendly Cython wrapping and installing function.
+# Builds a Cython module from the provided interface_header.
 # For example, for the interface header gtsam.h,
 # this will build the wrap module 'gtsam'.
 #
 # Arguments:
 #
 # interface_header:  The relative path to the wrapper interface definition file.
-# extra_imports: extra header to import in the Cython pxd file. 
-#                For example, to use Cython gtsam.pxd in your own module, 
+# 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
-function(wrap_and_install_library_cython interface_header extra_imports setup_py_in_path install_path)
+# dependencies: Dependencies which need to be built before the wrapper
+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}" "${setup_py_in_path}")
+  wrap_library_cython("${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)
+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*
@@ -45,36 +43,39 @@ function(wrap_library_cython interface_header generated_files_path extra_imports
   get_filename_component(module_name "${interface_header}" NAME_WE)
 
   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 ${generated_files_path})
-    
-  # Set up building of mex module
-  add_custom_target(${module_name}_cython_wrapper ALL DEPENDS ${generated_cpp_file} ${interface_header})
-    add_custom_target(wrap_${module_name}_cython_distclean 
+    WORKING_DIRECTORY ${generated_files_path}/../)
+  add_custom_target(${module_name}_cython_wrapper ALL DEPENDS ${generated_cpp_file} ${interface_header} ${dependencies})
+
+  # Set up building of cython module
+  find_package(PythonLibs 2.7 REQUIRED)
+  include_directories(${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()
 
@@ -96,8 +97,8 @@ function(install_cython_wrapped_library interface_header generated_files_path in
       # Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH if there is one
       get_filename_component(location "${install_path}" PATH)
       get_filename_component(name "${install_path}" NAME)
-      install(DIRECTORY "${generated_files_path}/" DESTINATION "${location}/${name}${build_type_tag}" 
-          CONFIGURATIONS "${build_type}" 
+      install(DIRECTORY "${generated_files_path}/" DESTINATION "${location}/${name}${build_type_tag}"
+          CONFIGURATIONS "${build_type}"
           PATTERN "build" EXCLUDE
           PATTERN "CMakeFiles" EXCLUDE
           PATTERN "Makefile" EXCLUDE
@@ -106,7 +107,7 @@ function(install_cython_wrapped_library interface_header generated_files_path in
           PATTERN "*.py" EXCLUDE)
     endforeach()
   else()
-    install(DIRECTORY "${generated_files_path}/" DESTINATION ${install_path} 
+    install(DIRECTORY "${generated_files_path}/" DESTINATION ${install_path}
         PATTERN "build" EXCLUDE
         PATTERN "CMakeFiles" EXCLUDE
         PATTERN "Makefile" EXCLUDE
@@ -157,7 +158,7 @@ endfunction()
 # should be installed to all build type toolboxes
 #
 # Arguments:
-#  source_files: The source files to be installed. 
+#  source_files: The source files to be installed.
 #  dest_directory: The destination directory to install to.
 function(install_cython_files source_files dest_directory)
 
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" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+
+endif ()
diff --git a/cython/gtsam/setup.py.in b/cython/gtsam/setup.py.in
deleted file mode 100644
index 1ae067690..000000000
--- a/cython/gtsam/setup.py.in
+++ /dev/null
@@ -1,24 +0,0 @@
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Build import cythonize
-import eigency
-import sys
-import os
-
-os.environ["CXX"] = "${CMAKE_CXX_COMPILER}"
-os.environ["CC"] = "${CMAKE_C_COMPILER}"
-
-setup(
-  ext_modules = cythonize(Extension(
-    "gtsam",
-    sources=["gtsam.pyx"],
-    include_dirs = ["${PROJECT_SOURCE_DIR}", "${CMAKE_BINARY_DIR}",
-                    "${PROJECT_SOURCE_DIR}/gtsam/3rdparty/Eigen",
-                    "${Boost_INCLUDE_DIR}"
-                    ] + eigency.get_includes(include_eigen=False),
-    libraries = ['gtsam${gtsam_library_postfix}'],
-    library_dirs = ["${CMAKE_CURRENT_BINARY_DIR}"],
-    language="c++",
-    extra_compile_args="${CMAKE_CXX_FLAGS}".split(),
-    extra_link_args="${CMAKE_SHARED_LINKER_FLAGS}".split()))
-)
diff --git a/cython/gtsam_unstable/setup.py.in b/cython/gtsam_unstable/setup.py.in
deleted file mode 100644
index d7057cec7..000000000
--- a/cython/gtsam_unstable/setup.py.in
+++ /dev/null
@@ -1,29 +0,0 @@
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Build import cythonize
-import eigency
-import sys
-import os
-
-# so that it can find the wrapped gtsam package
-sys.path.append("..")
-
-os.environ["CXX"] = "${CMAKE_CXX_COMPILER}"
-os.environ["CC"] = "${CMAKE_C_COMPILER}"
-
-setup(
-    ext_modules=cythonize(Extension(
-        "gtsam_unstable",
-        sources=["gtsam_unstable.pyx"],
-        include_dirs = ["${CMAKE_SOURCE_DIR}", "${CMAKE_BINARY_DIR}",
-                        "${CMAKE_SOURCE_DIR}/gtsam/3rdparty/Eigen",
-                        "${Boost_INCLUDE_DIR}"
-                       ] + eigency.get_includes(include_eigen=False),
-        libraries=['gtsam${gtsam_library_postfix}', 'gtsam_unstable${gtsam_library_postfix}'],
-        library_dirs = ["${CMAKE_BINARY_DIR}/gtsam",
-                        "${CMAKE_BINARY_DIR}/gtsam_unstable"],
-        language="c++",
-        extra_compile_args="${CMAKE_CXX_FLAGS}".split(),
-        extra_link_args="${CMAKE_SHARED_LINKER_FLAGS}".split()))
-)
-
diff --git a/gtsam/CMakeLists.txt b/gtsam/CMakeLists.txt
index eb9154091..ed80ff119 100644
--- a/gtsam/CMakeLists.txt
+++ b/gtsam/CMakeLists.txt
@@ -166,15 +166,3 @@ if (GTSAM_INSTALL_MATLAB_TOOLBOX)
     wrap_and_install_library(../gtsam.h "${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 
-                                    "${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
-                                    )
-endif ()
diff --git a/gtsam_unstable/CMakeLists.txt b/gtsam_unstable/CMakeLists.txt
index 7e26bca04..448e8b00e 100644
--- a/gtsam_unstable/CMakeLists.txt
+++ b/gtsam_unstable/CMakeLists.txt
@@ -118,20 +118,6 @@ if (GTSAM_INSTALL_MATLAB_TOOLBOX)
     wrap_and_install_library(gtsam_unstable.h "gtsam" "" "${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
-                                    )
-    add_dependencies(gtsam_unstable_cython_wrapper gtsam_cython_wrapper)
-endif ()
 
 # Build examples
 add_subdirectory(examples)