diff --git a/Makefile b/Makefile
index c3dc83c77..4f60d0d8b 100644
--- a/Makefile
+++ b/Makefile
@@ -25,7 +25,10 @@ makefiles = \
   misc/zsh/local.mk \
   misc/systemd/local.mk \
   misc/launchd/local.mk \
-  misc/upstart/local.mk
+  misc/upstart/local.mk \
+  doc/manual/local.mk \
+  doc/internal-api/local.mk \
+  doc/external-api/local.mk
 endif
 
 ifeq ($(ENABLE_UNIT_TESTS), yes)
diff --git a/configure.ac b/configure.ac
index 676b145a5..c3823c01c 100644
--- a/configure.ac
+++ b/configure.ac
@@ -150,6 +150,11 @@ AC_ARG_ENABLE(unit-tests, AS_HELP_STRING([--disable-unit-tests],[Do not build th
   ENABLE_UNIT_TESTS=$enableval, ENABLE_UNIT_TESTS=$ENABLE_BUILD)
 AC_SUBST(ENABLE_UNIT_TESTS)
 
+# Build external API docs by default
+AC_ARG_ENABLE(external_api_docs, AS_HELP_STRING([--enable-external-api-docs],[Build API docs for Nix's C interface]),
+  external_api_docs=$enableval, external_api_docs=yes)
+AC_SUBST(external_api_docs)
+
 AS_IF(
   [test "$ENABLE_BUILD" == "no" && test "$ENABLE_UNIT_TESTS" == "yes"],
   [AC_MSG_ERROR([Cannot enable unit tests when building overall is disabled. Please do not pass '--enable-unit-tests' or do not pass '--disable-build'.])])
diff --git a/doc/external-api/.gitignore b/doc/external-api/.gitignore
new file mode 100644
index 000000000..dab28b6b0
--- /dev/null
+++ b/doc/external-api/.gitignore
@@ -0,0 +1,3 @@
+/doxygen.cfg
+/html
+/latex
diff --git a/doc/external-api/doxygen.cfg.in b/doc/external-api/doxygen.cfg.in
new file mode 100644
index 000000000..19350b2c6
--- /dev/null
+++ b/doc/external-api/doxygen.cfg.in
@@ -0,0 +1,54 @@
+# Doxyfile 1.9.5
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME           = "Nix"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER         = @PACKAGE_VERSION@
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          = "Nix, the purely functional package manager; stable external interfaces"
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX         = NO
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+# FIXME Make this list more maintainable somehow. We could maybe generate this
+# in the Makefile, but we would need to change how `.in` files are preprocessed
+# so they can expand variables despite configure variables.
+
+INPUT                  = \
+  src/libutil \
+  src/libexpr \
+  src/libstore
+
+FILE_PATTERNS = nix_api_*.h
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor. Note that the INCLUDE_PATH is not recursive, so the setting of
+# RECURSIVE has no effect here.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           = @RAPIDCHECK_HEADERS@
+EXCLUDE_PATTERNS = *_internal.h
+GENERATE_TREEVIEW = YES
+OPTIMIZE_OUTPUT_FOR_C  = YES
diff --git a/doc/external-api/local.mk b/doc/external-api/local.mk
new file mode 100644
index 000000000..a0f6e26fc
--- /dev/null
+++ b/doc/external-api/local.mk
@@ -0,0 +1,19 @@
+.PHONY: external-api-html
+
+ifeq ($(internal_api_docs), yes)
+
+$(docdir)/external-api/html/index.html $(docdir)/external-api/latex: $(d)/doxygen.cfg
+	mkdir -p $(docdir)/external-api
+	{ cat $< ; echo "OUTPUT_DIRECTORY=$(docdir)/external-api" ; } | doxygen -
+
+# Generate the HTML API docs for Nix's unstable internal interfaces.
+external-api-html: $(docdir)/external-api/html/index.html
+
+else
+
+# Make a nicer error message
+external-api-html:
+	@echo "Internal API docs are disabled. Configure with '--enable-external-api-docs', or avoid calling 'make external-api-html'."
+	@exit 1
+
+endif
diff --git a/src/libexpr/nix_api_expr.h b/src/libexpr/nix_api_expr.h
index c56ef89bb..f67a3d13f 100644
--- a/src/libexpr/nix_api_expr.h
+++ b/src/libexpr/nix_api_expr.h
@@ -1,5 +1,26 @@
 #ifndef NIX_API_EXPR_H
 #define NIX_API_EXPR_H
+/** @defgroup libexpr libexpr
+ * @brief Bindings to the Nix evaluator
+ *
+ * Example (without error handling):
+ * @code{.c}
+ * int main() {
+ *    nix_libexpr_init(NULL);
+ *
+ *    Store* store = nix_store_open(NULL, "dummy", NULL);
+ *    State* state = nix_state_create(NULL, NULL /* empty NIX_PATH */, store);
+*Value *value = nix_alloc_value(NULL, state);
+**nix_expr_eval_from_string(NULL, state, "builtins.nixVersion", ".", value);
+*nix_value_force(NULL, state, value);
+*printf("nix version: %s\n", nix_get_string(NULL, value));
+**nix_gc_decref(NULL, value);
+*nix_state_free(state);
+*nix_store_unref(store);
+*return 0;
+*
+}
+*@endcode *@{* /
 /** @file
  * @brief Main entry for the libexpr C bindings
  */
@@ -8,22 +29,25 @@
 #include "nix_api_util.h"
 
 #ifdef __cplusplus
-extern "C" {
+             extern "C" {
 #endif
-// cffi start
+                 // cffi start
 
-// Type definitions
-/**
- * @brief Represents a nix evaluator state.
- *
- * Multiple can be created for multi-threaded
- * operation.
- */
-typedef struct State State; // nix::EvalState
+                 // Type definitions
+                 /**
+                  * @brief Represents a nix evaluator state.
+                  *
+                  * Multiple can be created for multi-threaded
+                  * operation.
+                  * @struct State
+                  */
+                 typedef struct State State; // nix::EvalState
 /**
  * @brief Represents a nix value.
  *
  * Owned by the GC.
+ * @struct Value
+ * @see value_manip
  */
 typedef void Value; // nix::Value
 
@@ -110,23 +134,36 @@ State *nix_state_create(nix_c_context *context, const char **searchPath,
  */
 void nix_state_free(State *state);
 
+/** @addtogroup GC
+ * @brief Reference counting and garbage collector operations
+ *
+ * Nix's evaluator uses a garbage collector. To ease C interop, we implement
+ * a reference counting scheme, where objects will be deallocated
+ * when there are no references from the Nix side, and the reference count kept
+ * by the C API reaches `0`.
+ *
+ * Functions returning a garbage-collected object will automatically increase
+ * the refcount for you. You should make sure to call `nix_gc_decref` when
+ * you're done.
+ * @{
+ */
 /**
  * @brief Increase the GC refcount.
  *
  * The nix C api keeps alive objects by refcounting.
  * When you're done with a refcounted pointer, call nix_gc_decref.
  *
- * Does not fail
- *
+ * @param[out] context Optional, stores error information
  * @param[in] object The object to keep alive
  */
-nix_err nix_gc_incref(nix_c_context *, const void *);
+nix_err nix_gc_incref(nix_c_context *context, const void *object);
 /**
  * @brief Decrease the GC refcount
  *
+ * @param[out] context Optional, stores error information
  * @param[in] object The object to stop referencing
  */
-nix_err nix_gc_decref(nix_c_context *, const void *);
+nix_err nix_gc_decref(nix_c_context *context, const void *object);
 
 /**
  * @brief Trigger the garbage collector manually
@@ -147,9 +184,12 @@ void nix_gc_now();
 void nix_gc_register_finalizer(void *obj, void *cd,
                                void (*finalizer)(void *obj, void *cd));
 
+/** @} */
 // cffi end
 #ifdef __cplusplus
 }
 #endif
 
+/** @} */
+
 #endif // NIX_API_EXPR_H
diff --git a/src/libexpr/nix_api_external.h b/src/libexpr/nix_api_external.h
index 45e95346b..692f8000c 100644
--- a/src/libexpr/nix_api_external.h
+++ b/src/libexpr/nix_api_external.h
@@ -1,5 +1,10 @@
 #ifndef NIX_API_EXTERNAL_H
 #define NIX_API_EXTERNAL_H
+/** @ingroup libexpr
+ * @addtogroup Externals
+ * @brief Deal with external values
+ * @{
+ */
 /** @file
  * @brief libexpr C bindings dealing with external values
  */
@@ -184,5 +189,6 @@ void *nix_get_external_value_content(nix_c_context *context, ExternalValue *b);
 #ifdef __cplusplus
 }
 #endif
+/** @} */
 
 #endif // NIX_API_EXTERNAL_H
diff --git a/src/libexpr/nix_api_value.h b/src/libexpr/nix_api_value.h
index 8fa85b25d..110dd086f 100644
--- a/src/libexpr/nix_api_value.h
+++ b/src/libexpr/nix_api_value.h
@@ -1,6 +1,9 @@
 #ifndef NIX_API_VALUE_H
 #define NIX_API_VALUE_H
 
+/** @addtogroup libexpr
+ * @{
+ */
 /** @file
  * @brief libexpr C bindings dealing with values
  */
@@ -35,6 +38,7 @@ typedef void Value;
 typedef struct State State;
 // type defs
 /** @brief Stores an under-construction set of bindings
+ * @ingroup value_manip
  *
  * Do not reuse.
  * @see nix_make_bindings_builder, nix_bindings_builder_free, nix_make_attrs
@@ -43,18 +47,23 @@ typedef struct State State;
 typedef struct BindingsBuilder BindingsBuilder;
 
 /** @brief PrimOp function
+ * @ingroup primops
  *
  * Owned by the GC
  * @see nix_alloc_primop, nix_set_primop
  */
 typedef struct PrimOp PrimOp;
 /** @brief External Value
+ * @ingroup Externals
  *
  * Owned by the GC
- * @see nix_api_external.h
  */
 typedef struct ExternalValue ExternalValue;
 
+/** @defgroup primops
+ * @brief Create your own primops
+ * @{
+ */
 /** @brief Function pointer for primops
  * @param[in] state Evaluator state
  * @param[in] pos position of function call
@@ -79,6 +88,7 @@ typedef void (*PrimOpFun)(State *state, int pos, Value **args, Value *v);
  */
 PrimOp *nix_alloc_primop(nix_c_context *context, PrimOpFun fun, int arity,
                          const char *name, const char **args, const char *doc);
+/** @} */
 
 // Function prototypes
 
@@ -91,6 +101,10 @@ PrimOp *nix_alloc_primop(nix_c_context *context, PrimOpFun fun, int arity,
  *
  */
 Value *nix_alloc_value(nix_c_context *context, State *state);
+/** @addtogroup value_manip Manipulating values
+ * @brief Functions to inspect and change nix Value's
+ * @{
+ */
 /** @name Getters
  */
 /**@{*/
@@ -328,10 +342,12 @@ nix_err nix_bindings_builder_insert(nix_c_context *context,
  * @param[in] builder the builder to free
  */
 void nix_bindings_builder_free(BindingsBuilder *builder);
+/**@}*/
 
 // cffi end
 #ifdef __cplusplus
 }
 #endif
 
+/** @} */
 #endif // NIX_API_VALUE_H
diff --git a/src/libstore/nix_api_store.h b/src/libstore/nix_api_store.h
index 6157faa82..bc01f0ad2 100644
--- a/src/libstore/nix_api_store.h
+++ b/src/libstore/nix_api_store.h
@@ -1,5 +1,12 @@
 #ifndef NIX_API_STORE_H
 #define NIX_API_STORE_H
+/**
+ * @defgroup libstore libstore
+ * @brief C bindings for nix libstore
+ *
+ * libstore is used for talking to a Nix store
+ * @{
+ */
 /** @file
  * @brief Main entry for the libstore C bindings
  */
@@ -121,5 +128,7 @@ nix_err nix_store_get_version(nix_c_context *, Store *store, char *dest,
 #ifdef __cplusplus
 }
 #endif
-
+/**
+ * @}
+ */
 #endif // NIX_API_STORE_H
diff --git a/src/libutil/nix_api_util.h b/src/libutil/nix_api_util.h
index 095564296..f626f2ccb 100644
--- a/src/libutil/nix_api_util.h
+++ b/src/libutil/nix_api_util.h
@@ -1,6 +1,13 @@
 #ifndef NIX_API_UTIL_H
 #define NIX_API_UTIL_H
-
+/**
+ * @defgroup libutil libutil
+ * @brief C bindings for nix libutil
+ *
+ * libutil is used for functionality shared between
+ * different Nix modules.
+ * @{
+ */
 /** @file
  * @brief Main entry for the libutil C bindings
  *
@@ -12,6 +19,31 @@ extern "C" {
 #endif
 // cffi start
 
+/** @defgroup errors Handling errors
+ * @brief Dealing with errors from the Nix side
+ *
+ * To handle errors that can be returned from the Nix API
+ * nix_c_context can be passed any function that potentially returns an error.
+ *
+ * Error information will be stored in this context, and can be retrieved
+ * using nix_err_code, nix_err_msg.
+ *
+ * Passing NULL instead will cause the API to throw C++ errors.
+ *
+ * Example:
+ * @code{.c}
+ * int main() {
+ *     nix_c_context* ctx = nix_c_context_create();
+ *     nix_libutil_init(ctx);
+ *     if (nix_err_code(ctx) != NIX_OK) {
+ *         printf("error: %s\n", nix_err_msg(NULL, ctx, NULL));
+ *         return 1;
+ *     }
+ *     return 0;
+ * }
+ * @endcode
+ *  @{
+ */
 // Error codes
 /**
  * @brief Type for error codes in the NIX system
@@ -67,6 +99,7 @@ typedef int nix_err;
 
 /**
  * @brief This object stores error state.
+ * @struct nix_c_context
  *
  * Passed as a first parameter to C functions that can fail, will store error
  * information. Optional wherever it is used, passing NULL will throw a C++
@@ -92,6 +125,9 @@ nix_c_context *nix_c_context_create();
  * @param[out] context The context to free, mandatory.
  */
 void nix_c_context_free(nix_c_context *context);
+/**
+ *  @}
+ */
 
 /**
  * @brief Initializes nix_libutil and its dependencies.
@@ -105,6 +141,9 @@ void nix_c_context_free(nix_c_context *context);
  */
 nix_err nix_libutil_init(nix_c_context *context);
 
+/** @defgroup settings
+ *  @{
+ */
 /**
  * @brief Retrieves a setting from the nix global configuration.
  *
@@ -128,8 +167,8 @@ nix_err nix_setting_get(nix_c_context *context, const char *key, char *value,
  *
  * Use "extra-<setting name>" to append to the setting's value.
  *
- * Settings only apply for new States. Call nix_plugins_init() when you are done
- * with the settings to load any plugins.
+ * Settings only apply for new State%s. Call nix_plugins_init() when you are
+ * done with the settings to load any plugins.
  *
  * @param[out] context optional, Stores error information
  * @param[in] key The key of the setting to set.
@@ -140,6 +179,9 @@ nix_err nix_setting_get(nix_c_context *context, const char *key, char *value,
 nix_err nix_setting_set(nix_c_context *context, const char *key,
                         const char *value);
 
+/**
+ *  @}
+ */
 // todo: nix_plugins_init()
 
 /**
@@ -150,6 +192,9 @@ nix_err nix_setting_set(nix_c_context *context, const char *key,
  */
 const char *nix_version_get();
 
+/** @addtogroup errors
+ *  @{
+ */
 /**
  * @brief Retrieves the most recent error message from a context.
  *
@@ -215,9 +260,14 @@ nix_err nix_err_name(nix_c_context *context, const nix_c_context *read_context,
  */
 nix_err nix_err_code(nix_c_context *context, const nix_c_context *read_context);
 
+/**
+ *  @}
+ */
+
 // cffi end
 #ifdef __cplusplus
 }
 #endif
 
+/** @} */
 #endif // NIX_API_UTIL_H