diff --git a/.codedocs b/.codedocs
index 60279fa..03ef774 100644
--- a/.codedocs
+++ b/.codedocs
@@ -188,6 +188,6 @@ TAGLINKS =
 # TYPEDEF_HIDES_STRUCT =
 # UML_LIMIT_NUM_FIELDS =
 # UML_LOOK =
-USE_MDFILE_AS_MAINPAGE = doc/API.md
+# USE_MDFILE_AS_MAINPAGE =
 # VERBATIM_HEADERS =
 #
diff --git a/configure.ac b/configure.ac
index 5afd2d3..4367749 100644
--- a/configure.ac
+++ b/configure.ac
@@ -5,7 +5,8 @@ AM_SILENT_RULES([yes])
 
 AC_CONFIG_SRCDIR(src/uev.c)
 AC_CONFIG_HEADERS(config.h)
-AC_CONFIG_FILES([Makefile doc/Makefile examples/Makefile src/libuev.pc src/Makefile tests/Makefile])
+AC_CONFIG_FILES([Makefile doc/Makefile doc/Doxyfile examples/Makefile
+			  src/libuev.pc src/Makefile tests/Makefile])
 AC_CONFIG_MACRO_DIR([m4])
 
 AC_PROG_CC
diff --git a/doc/.gitignore b/doc/.gitignore
index 4a1faaa..de8e7b6 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -1,2 +1,3 @@
 html/*
 libuev.tag
+Doxyfile
diff --git a/doc/Doxyfile b/doc/Doxyfile.in
similarity index 99%
rename from doc/Doxyfile
rename to doc/Doxyfile.in
index 3d74d9b..cbe571c 100644
--- a/doc/Doxyfile
+++ b/doc/Doxyfile.in
@@ -32,13 +32,13 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "libuEv"
+PROJECT_NAME           = @PACKAGE_NAME@
 
 # 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         =
+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
@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = ./
+OUTPUT_DIRECTORY       = @top_builddir@/doc
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -829,7 +829,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../src/ ../README.md API.md
+INPUT                  = @top_srcdir@/src/ @top_srcdir@/README.md @top_srcdir@/doc/API.md
 
 # 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
@@ -917,7 +917,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = ../src/bench.c ../src/private.h ../src/README.md
+EXCLUDE                = @top_srcdir@/src/bench.c @top_srcdir@/src/private.h @top_srcdir@/src/README.md
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -1026,7 +1026,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = API.md
+USE_MDFILE_AS_MAINPAGE = @top_srcdir@/doc/API.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
diff --git a/doc/Makefile.am b/doc/Makefile.am
index 9c075c3..1930ed6 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -1,5 +1,5 @@
 dist_doc_DATA = API.md
-EXTRA_DIST    = Doxyfile
+EXTRA_DIST    = Doxyfile.in
 
 if ENABLE_HTML
 pkghtmldir     = $(docdir)/html