Doxygen uses cmake (http://www.cmake.org/) to build executables for various platforms. It's required at least cmake version 2.8.12 The first step is to create a build directory where the output should be stored. Doxygen can be fully build outside of the source tree. The second step is to invoke cmake from within the build directory with the desired generator. For Linux/Unix systems do the following mkdir build cd build cmake -G "Unix Makefiles" path/to/root/of/doxygen/source/tree make This also works for MacOSX, but if XCode is installed you can also generate an XCode project file cmake -G XCode path/to/root/of/doxygen/source/tree For Windows one can generate a Visual Studio project using cmake -G "Visual Studio 12 2013" path\to\root\of\doxygen\source\tree (this is for Visual Studio 12, there are typically also generators for other versions of Visual Studio or other compiler environments like MinGW) Doxygen's cmake configuration provides a number of options: - build_wizard Build the GUI frontend for doxygen. - build_app Example showing how to embed doxygen in an application. - build_parse Parses source code and dumps the dependencies between the code elements. - build_xmlparser Example showing how to parse doxygen's XML output. - build_search Build external search tools (doxysearch and doxyindexer). - build_doc Build user manual. - use_sqlite3 Add support for sqlite3 output [experimental]. - use_libclang Add support for libclang parsing. - win_static Link with /MT in stead of /MD on windows. - english_only Only compile in support for the English language. - force_qt4 Forces doxywizard to build using Qt4 even if Qt5 is installed An option can be turned on, by adding -D<option>=ON as a command line option, this can be done when generating the initial build files, but also afterwards, i.e. to enable building of the documentation after an initial cmake -G run, do cmake -Dbuild_doc=ON path/to/root/of/doxygen/source/tree To turn the option off use cmake -Dbuild_doc=OFF path/to/root/of/doxygen/source/tree To see the current value is of the various options, you can run cmake -L path/to/root/of/doxygen/source/tree The build target for building the documentation is 'docs' and the build target for the regression tests is 'tests'