diff --git a/.travis.yml b/.travis.yml
index f30a4e3..dbc2347 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,6 +9,7 @@
 - tests/scripts/check-generated-files.sh
 - tests/scripts/check-doxy-blocks.pl
 - tests/scripts/check-names.sh
+- tests/scripts/doxygen.sh
 - cmake -D CMAKE_BUILD_TYPE:String="Check" .
 - make
 - make test
@@ -23,6 +24,10 @@
     secure: "barHldniAfXyoWOD/vcO+E6/Xm4fmcaUoC9BeKW+LwsHqlDMLvugaJnmLXkSpkbYhVL61Hzf3bo0KPJn88AFc5Rkf8oYHPjH4adMnVXkf3B9ghHCgznqHsAH3choo6tnPxaFgOwOYmLGb382nQxfE5lUdvnM/W/psQjWt66A1+k="
 
 addons:
+  apt:
+    packages:
+    - doxygen
+    - graphviz
   coverity_scan:
     project:
       name: "ARMmbed/mbedtls"
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8905218..094d906 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -85,20 +85,9 @@
     add_subdirectory(programs)
 endif()
 
-# targets for doxygen only work on Unix
-if(UNIX)
-    ADD_CUSTOM_TARGET(apidoc
-        COMMAND mkdir -p apidoc
-        COMMAND cp include/mbedtls/config.h include/mbedtls/config.h.bak
-        COMMAND scripts/config.pl realfull
-        COMMAND doxygen doxygen/mbedtls.doxyfile
-        COMMAND mv include/mbedtls/config.h.bak include/mbedtls/config.h
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-
-    ADD_CUSTOM_TARGET(apidoc_clean
-        COMMAND rm -rf apidoc
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-endif(UNIX)
+ADD_CUSTOM_TARGET(apidoc
+    COMMAND doxygen doxygen/mbedtls.doxyfile
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 
 if(ENABLE_TESTING)
     enable_testing()
diff --git a/ChangeLog b/ChangeLog
index f68333e..71aa605 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -6,6 +6,8 @@
    * Fix bug in mbedtls_mpi_add_mpi() that caused wrong results when the three
      arguments where the same (in-place doubling). Found and fixed by Janos
      Follath. #309
+   * Fix potential build failures related to the 'apidoc' target, introduced
+     in the previous patch release. Found by Robert Scheck. #390 #391
    * Fix issue in Makefile that prevented building using armar. #386
 
 Changes
diff --git a/Makefile b/Makefile
index 0950e6b..7f03115 100644
--- a/Makefile
+++ b/Makefile
@@ -87,10 +87,7 @@
 
 apidoc:
 	mkdir -p apidoc
-	cp include/mbedtls/config.h include/mbedtls/config.h.bak
-	scripts/config.pl realfull
 	doxygen doxygen/mbedtls.doxyfile
-	mv include/mbedtls/config.h.bak include/mbedtls/config.h
 
 apidoc_clean:
 	rm -rf apidoc
diff --git a/doxygen/mbedtls.doxyfile b/doxygen/mbedtls.doxyfile
index 6a00f47..2fc0b7f 100644
--- a/doxygen/mbedtls.doxyfile
+++ b/doxygen/mbedtls.doxyfile
@@ -696,7 +696,7 @@
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = configs
+EXCLUDE                = configs yotta/module
 
 # 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
@@ -710,7 +710,7 @@
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = *_internal.h *_wrap.h
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -1485,13 +1485,13 @@
 # which can be used by a validating XML parser to check the
 # syntax of the XML files.
 
-XML_SCHEMA             =
+#XML_SCHEMA             =
 
 # The XML_DTD tag can be used to specify an XML DTD,
 # which can be used by a validating XML parser to check the
 # syntax of the XML files.
 
-XML_DTD                =
+#XML_DTD                =
 
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will
 # dump the program listings (including syntax highlighting
diff --git a/scripts/apidoc_full.sh b/scripts/apidoc_full.sh
new file mode 100755
index 0000000..bebab10
--- /dev/null
+++ b/scripts/apidoc_full.sh
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+# Generate doxygen documentation with a full config.h (this ensures that every
+# available flag is documented, and avoids warnings about documentation
+# without a corresponding #define).
+#
+# /!\ This must not be a Makefile target, as it would create a race condition
+# when multiple targets are invoked in the same parallel build.
+
+set -eu
+
+CONFIG_H='include/mbedtls/config.h'
+
+if [ -r $CONFIG_H ]; then :; else
+    echo "$CONFIG_H not found" >&2
+    exit 1
+fi
+
+CONFIG_BAK=${CONFIG_H}.bak
+cp -p $CONFIG_H $CONFIG_BAK
+
+scripts/config.pl realfull
+make apidoc
+
+mv $CONFIG_BAK $CONFIG_H
diff --git a/tests/scripts/all.sh b/tests/scripts/all.sh
index 4829c8f..2f716bb 100755
--- a/tests/scripts/all.sh
+++ b/tests/scripts/all.sh
@@ -21,12 +21,16 @@
 CONFIG_BAK="$CONFIG_H.bak"
 
 MEMORY=0
+SHORT=0
 
 while [ $# -gt 0 ]; do
     case "$1" in
         -m*)
             MEMORY=${1#-m}
             ;;
+        -s)
+            SHORT=1
+            ;;
         *)
             echo "Unknown argument: '$1'" >&2
             echo "Use the source, Luke!" >&2
@@ -83,6 +87,12 @@
 cleanup
 tests/scripts/check-names.sh
 
+if which doxygen >/dev/null; then
+    msg "test: doxygen warnings" # ~ 3s
+    cleanup
+    tests/scripts/doxygen.sh
+fi
+
 msg "build: create and build yotta module" # ~ 30s
 cleanup
 tests/scripts/yotta-build.sh
@@ -103,6 +113,11 @@
 tests/scripts/test-ref-configs.pl
 
 # Most frequent issues are likely to be caught at this point
+if [ $SHORT -eq 1 ]; then
+    msg "Done, cleaning up"
+    cleanup
+    exit 0
+fi
 
 msg "build: with ASan (rebuild after ref-configs)" # ~ 1 min
 make
diff --git a/tests/scripts/doxygen.sh b/tests/scripts/doxygen.sh
new file mode 100755
index 0000000..e7758c9
--- /dev/null
+++ b/tests/scripts/doxygen.sh
@@ -0,0 +1,29 @@
+#!/bin/sh
+
+# Make sure the doxygen documentation builds without warnings
+
+# Abort on errors (and uninitiliased variables)
+set -eu
+
+if [ -d library -a -d include -a -d tests ]; then :; else
+    echo "Must be run from mbed TLS root" >&2
+    exit 1
+fi
+
+if scripts/apidoc_full.sh > doc.out 2>doc.err; then :; else
+    cat doc.err
+    echo "FAIL" >&2
+    exit 1;
+fi
+
+cat doc.out doc.err | \
+    grep -v "warning: ignoring unsupported tag" \
+    > doc.filtered
+
+if egrep "(warning|error):" doc.filtered; then
+    echo "FAIL" >&2
+    exit 1;
+fi
+
+make apidoc_clean
+rm -f doc.out doc.err doc.filtered