diff --git a/configure.ac b/configure.ac
index 75561cda..3e9365ab 100644
--- a/configure.ac
+++ b/configure.ac
@@ -431,6 +431,7 @@ AC_CONFIG_FILES([ \
 	include/share/Makefile \
 	include/share/grabbag/Makefile \
 	include/test_libs_common/Makefile \
+	doc/Doxyfile \
 	doc/Makefile \
 	doc/html/Makefile \
 	doc/html/images/Makefile \
diff --git a/doc/Doxyfile b/doc/Doxyfile.in
similarity index 99%
rename from doc/Doxyfile
rename to doc/Doxyfile.in
index 000c2fb9..94805456 100644
--- a/doc/Doxyfile
+++ b/doc/Doxyfile.in
@@ -451,8 +451,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = ../include/FLAC \
-                         ../include/FLAC++
+INPUT                  = @top_srcdir@/include/FLAC \
+                         @top_srcdir@/include/FLAC++
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
@@ -632,7 +632,7 @@ HTML_HEADER            =
 # each generated HTML page. If it is left blank doxygen will generate a 
 # standard footer.
 
-HTML_FOOTER            = doxygen.footer.html
+HTML_FOOTER            = @top_srcdir@/doc/doxygen.footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
 # style sheet that is used by each HTML page. It can be used to 
diff --git a/doc/Makefile.am b/doc/Makefile.am
index 70fb4a14..67703e9e 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -18,6 +18,7 @@
 SUBDIRS = . html
 
 if FLaC__HAS_DOXYGEN
+all-local: Doxyfile
 FLAC.tag: Doxyfile
 	doxygen Doxyfile
 	rm -rf html/api
@@ -35,7 +36,7 @@ docdir = $(datadir)/doc/$(PACKAGE)-$(VERSION)
 doc_DATA = \
 	FLAC.tag
 
-EXTRA_DIST = Doxyfile Makefile.lite doxygen.footer.html doxygen.header.html $(doc_DATA)
+EXTRA_DIST = Doxyfile.in Makefile.lite doxygen.footer.html doxygen.header.html $(doc_DATA)
 
 maintainer-clean-local:
 	rm -rf FLAC.tag html/api doxytmp
diff --git a/doc/html/Makefile.am b/doc/html/Makefile.am
index 1b2b3363..2b06aab6 100644
--- a/doc/html/Makefile.am
+++ b/doc/html/Makefile.am
@@ -72,7 +72,7 @@ if FLaC__HAS_DOXYGEN
 # handle 'api/' specially:
 install-data-local:
 	$(mkinstalldirs) $(DESTDIR)$(docdir)/api
-	(cd $(srcdir)/api && $(INSTALL_DATA) * $(DESTDIR)$(docdir)/api)
+	(cd $(builddir)/api && $(INSTALL_DATA) * $(DESTDIR)$(docdir)/api)
 uninstall-local:
 	rm -rf $(DESTDIR)$(docdir)/api
 maintainer-clean-local: