diff --git a/Makefile.am b/Makefile.am
index 1a84cbbdf..ec38cf4ea 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1102,7 +1102,8 @@ endif
 
 doc/api/html/index.html: doc/doxygen.conf
 	@mkdir -p $(@D)
-	$(DOXYGEN) $<
+	[ "$(srcdir)" = "." ] || sed '/INPUT *=/ s/\([^ ]\+\/\)/$(subst /,\/,$(srcdir))\/\1/g' $(srcdir)/doc/doxygen.conf >doc/doxygen.conf
+	$(DOXYGEN) doc/doxygen.conf
 
 all-local: $(DOCBOOK_HTML) doc/api/html/index.html
 
diff --git a/doc/doxygen.conf b/doc/doxygen.conf
index 625e070ae..ddece77e8 100644
--- a/doc/doxygen.conf
+++ b/doc/doxygen.conf
@@ -534,7 +534,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = src
+INPUT = 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, which is