diff --git a/.gitignore b/.gitignore
index 007d4c7..8298f14 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+/.idea
 /build
 /dist
 /setools.egg-info
@@ -6,8 +7,7 @@
 libqpol/policy_parse.c
 libqpol/policy_parse.h
 libqpol/policy_scan.c
-setools/policyrep/qpol_wrap.c
-setools/policyrep/qpol.py
+/setools/policyrep/libpolicyrep.c
 *.so
 
 # Qt Generated Help files
diff --git a/MANIFEST.in b/MANIFEST.in
index a7d6576..ef886da 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -7,6 +7,8 @@ include libqpol/include/qpol/*.h
 include man/*
 include qhc/*
 include setools/perm_map
+include setools/policyrep/*.pxi
+include setools/policyrep/libpolicyrep.pyx
 include setoolsui/*.ui
 include setoolsui/apol/*.ui
 include setoolsui/apol/apol.qhc
diff --git a/README.md b/README.md
index caf4d0d..1463940 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ addition to the development packages from the above list:
 * bison
 * flex
 * libsepol 2.7+
-* SWIG 2.0.12+ or 3.0+ (3.0.8+ required for Python 3.5)
+* cython 0.27+
 
 To run SETools unit tests, the following packages are required, in
 addition to the above dependencies:
diff --git a/setup.py b/setup.py
index 87781fc..cc1397e 100644
--- a/setup.py
+++ b/setup.py
@@ -12,6 +12,7 @@ import sys
 import os
 from os.path import join
 from contextlib import suppress
+from Cython.Build import cythonize
 
 
 class QtHelpCommand(Command):
@@ -107,8 +108,8 @@ if sys.platform.startswith('darwin'):
 else:
     macros=[]
 
-ext_py_mods = [Extension('setools.policyrep._qpol',
-                         ['setools/policyrep/qpol.i',
+ext_py_mods = [Extension('setools.policyrep.libpolicyrep',
+                         ['setools/policyrep/libpolicyrep.pyx',
                           'libqpol/avrule_query.c',
                           'libqpol/bool_query.c',
                           'libqpol/bounds_query.c',
@@ -155,14 +156,11 @@ ext_py_mods = [Extension('setools.policyrep._qpol',
                                              '-Wnested-externs',
                                              '-Wold-style-definition',
                                              '-Wpointer-arith',
-                                             '-Wredundant-decls',
                                              '-Wstrict-prototypes',
                                              '-Wunknown-pragmas',
                                              '-Wwrite-strings',
-                                             '-Wno-missing-field-initializers', # SWIG 3.0.2 generates partially-initialized structs
-                                             '-Wno-unused-parameter', # SWIG generates functions with unused parameters
+                                             '-Wno-sign-compare', # Bison
                                              '-Wno-cast-qual', # libsepol uses const-to-nonconst casts
-                                             '-Wno-shadow', # SWIG generates shadow variables
                                              '-Wno-unreachable-code', # Bison generates unreachable code
                                              '-fno-exceptions'],
                          swig_opts=['-Ilibqpol/include'],
@@ -183,7 +181,7 @@ setup(name='setools',
       scripts=['apol', 'sediff', 'seinfo', 'seinfoflow', 'sesearch', 'sedta'],
       data_files=[(join(sys.prefix, 'share/man/man1'), glob.glob("man/*.1"))],
       package_data={'': ['*.ui', '*.qhc', '*.qch'], 'setools': ['perm_map']},
-      ext_modules=ext_py_mods,
+      ext_modules=cythonize(ext_py_mods),
       test_suite='tests',
       license='GPLv2+, LGPLv2.1+',
       classifiers=[
diff --git a/tox.ini b/tox.ini
index d3d1fbe..d7d5cc0 100644
--- a/tox.ini
+++ b/tox.ini
@@ -20,6 +20,7 @@ commands        = pep8 --version
 [testenv:coverage]
 deps            = networkx==2.0
                   coverage
+                  cython>=0.27
 commands        = coverage --version
                   coverage erase
                   coverage run setup.py test
@@ -28,6 +29,7 @@ commands        = coverage --version
 [testenv:lint]
 deps            = pylint
                   networkx==2.0
+                  cython>=0.27
 commands        = {envpython} setup.py build_ext -i
                   pylint --version
                   pylint -E --rcfile .pylintrc setools tests seinfo seinfoflow sedta sesearch sediff
@@ -36,5 +38,6 @@ commands        = {envpython} setup.py build_ext -i
 
 [testenv]
 deps            = networkx==2.0
+                  cython>=0.27
 commands        = {envpython} setup.py test
 recreate        = True