diff --git a/CMakeLists.txt b/CMakeLists.txt
index 55448e2e..75879343 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -20,3 +20,14 @@ endif(Boost_FOUND)
 
 include_directories(${marian_SOURCE_DIR}/src)
 add_subdirectory(src)
+
+# add a target to generate API documentation with Doxygen
+find_package(Doxygen)
+if(DOXYGEN_FOUND)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+    add_custom_target(doc ALL
+        ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMENT "Generating API documentation with Doxygen" VERBATIM
+    )
+endif(DOXYGEN_FOUND)
diff --git a/Doxyfile b/Doxyfile.in
similarity index 99%
rename from Doxyfile
rename to Doxyfile.in
index 0e1a68ce..e82982ff 100644
--- a/Doxyfile
+++ b/Doxyfile.in
@@ -743,7 +743,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src
+INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/README.md b/README.md
index 67685375..7026c615 100644
--- a/README.md
+++ b/README.md
@@ -29,3 +29,6 @@ Compilation with `cmake > 3.5`:
     cmake ..
     make -j
 
+To compile API documentation using Doxygen, first cd to the build directory, and then:
+
+    make doc