diff --git a/docs/api/analysis_api.rst b/docs/api/analysis_api.rst
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+++ b/docs/api/analysis_api.rst
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+.. _API_analysis:
+
+.. automodule:: yank.analyze
+   :members:
+   :inherited-members:
diff --git a/docs/api/experiment_api.rst b/docs/api/experiment_api.rst
new file mode 100644
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+++ b/docs/api/experiment_api.rst
@@ -0,0 +1,5 @@
+.. _API_experiment:
+
+.. automodule:: yank.experiment
+   :members:
+   :inherited-members:
diff --git a/docs/api/index.rst b/docs/api/index.rst
new file mode 100644
index 00000000..c2b07ba4
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+++ b/docs/api/index.rst
@@ -0,0 +1,30 @@
+.. _API:
+
+#############
+API Reference
+#############
+
+YANK's API allows users to setup and run their own simulations in programmatic ways. If you would rather run YANK with
+YAML input files, please see the command line interface and the YAML options.
+
+.. toctree::
+   :maxdepth: 2
+
+   analysis_api
+   experiment_api
+   mpi_api
+   multistate_api/index
+   pipeline_api
+   restraints_api
+   utils_api
+   yank_api
+
+
+UML class diagram
+=================
+
+This UML diagram is a minimal representation of YANK's structure. This is not meant to be a comprehensive and accurate
+representation of the API, but only to provide a visual overview of the relationships between the available classes
+available, their role, and the way the interact with the OpenMMTools framework.
+
+.. figure:: site-resources/images/YANKUMLClassDiagram.png
diff --git a/docs/api/mpi_api.rst b/docs/api/mpi_api.rst
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+++ b/docs/api/mpi_api.rst
@@ -0,0 +1,5 @@
+.. _API_mpi:
+
+.. automodule:: yank.mpi
+   :members:
+   :inherited-members:
diff --git a/docs/api/multistate_api/analyzers_api.rst b/docs/api/multistate_api/analyzers_api.rst
new file mode 100644
index 00000000..8a1a4850
--- /dev/null
+++ b/docs/api/multistate_api/analyzers_api.rst
@@ -0,0 +1,5 @@
+.. _API_analyzer:
+
+.. automodule:: yank.multistate.multistateanalyzer
+   :members:
+   :inherited-members:
diff --git a/docs/api/multistate_api/index.rst b/docs/api/multistate_api/index.rst
new file mode 100644
index 00000000..b394e3dd
--- /dev/null
+++ b/docs/api/multistate_api/index.rst
@@ -0,0 +1,35 @@
+.. _API_multistate:
+
+#################
+MultiState Module
+#################
+
+This is the API for the Multi State sub-module and its classes.
+
+.. toctree::
+   :maxdepth: 2
+
+   analyzers_api
+
+
+.. _API_multistate_head:
+
+.. automodule:: yank.multistate
+   :members:
+   :inherited-members:
+
+.. automodule:: yank.multistate.multistatesampler
+   :members:
+   :inherited-members:
+
+.. automodule:: yank.multistate.replicaexchange
+   :members:
+   :inherited-members:
+
+.. automodule:: yank.multistate.paralleltempering
+   :members:
+   :inherited-members:
+
+.. automodule:: yank.multistate.sams
+   :members:
+   :inherited-members:
diff --git a/docs/api/pipeline_api.rst b/docs/api/pipeline_api.rst
new file mode 100644
index 00000000..86e4e130
--- /dev/null
+++ b/docs/api/pipeline_api.rst
@@ -0,0 +1,5 @@
+.. _API_pipeline:
+
+.. automodule:: yank.pipeline
+   :members:
+   :inherited-members:
diff --git a/docs/api/restraints_api.rst b/docs/api/restraints_api.rst
new file mode 100644
index 00000000..cb337e68
--- /dev/null
+++ b/docs/api/restraints_api.rst
@@ -0,0 +1,5 @@
+.. _API_restraints:
+
+.. automodule:: yank.restraints
+   :members:
+   :inherited-members:
diff --git a/docs/api/utils_api.rst b/docs/api/utils_api.rst
new file mode 100644
index 00000000..73ff7ca8
--- /dev/null
+++ b/docs/api/utils_api.rst
@@ -0,0 +1,5 @@
+.. _API_utils:
+
+.. automodule:: yank.utils
+   :members:
+   :inherited-members:
diff --git a/docs/api/yank_api.rst b/docs/api/yank_api.rst
new file mode 100644
index 00000000..d3097d61
--- /dev/null
+++ b/docs/api/yank_api.rst
@@ -0,0 +1,5 @@
+.. _API_yank:
+
+.. automodule:: yank.yank
+   :members:
+   :inherited-members: