diff --git a/dumux/multidomain/2cnistokes2p2cni/Makefile.am b/dumux/multidomain/2cnistokes2p2cni/Makefile.am
index 3b00952d826db0da1f73bc6e875e09b37cf2c456..003f38efe6c4c8664289e969085b5812df43d4bc 100644
--- a/dumux/multidomain/2cnistokes2p2cni/Makefile.am
+++ b/dumux/multidomain/2cnistokes2p2cni/Makefile.am
@@ -1,4 +1,8 @@
 2cnistokes2p2cnidir = $(includedir)/dumux/multidomain/2cnistokes2p2cni
 2cnistokes2p2cni_HEADERS = *.hh
 
+if !HAVE_DUNE_MULTIDOMAIN
+headercheck_IGNORE = 2cnistokes2p2cnilocaloperator.hh
+endif
+
 include $(top_srcdir)/am/global-rules
diff --git a/dumux/multidomain/2cstokes2p2c/Makefile.am b/dumux/multidomain/2cstokes2p2c/Makefile.am
index 1a0b3372869717cfffcf42b5a12dea68609681aa..347b9a51481119589d025e63a9024026029f43d3 100644
--- a/dumux/multidomain/2cstokes2p2c/Makefile.am
+++ b/dumux/multidomain/2cstokes2p2c/Makefile.am
@@ -1,4 +1,10 @@
 2cstokes2p2cdir = $(includedir)/dumux/multidomain/2cstokes2p2c
 2cstokes2p2c_HEADERS = *.hh
 
+if !HAVE_DUNE_MULTIDOMAIN
+headercheck_IGNORE = \
+  2cstokes2p2clocaloperator.hh \
+  2cstokes2p2cnewtoncontroller.hh
+endif
+
 include $(top_srcdir)/am/global-rules
diff --git a/dumux/multidomain/common/Makefile.am b/dumux/multidomain/common/Makefile.am
index 1c56fe2ecadbe9cc1c8a185370bcdcfbb131c523..ada66d91e8fdd95a6af4997da72d0551fef906d2 100644
--- a/dumux/multidomain/common/Makefile.am
+++ b/dumux/multidomain/common/Makefile.am
@@ -1,4 +1,20 @@
 commondir = $(includedir)/dumux/multidomain/common
 common_HEADERS = *.hh
 
+if !HAVE_DUNE_MULTIDOMAIN
+headercheck_IGNORE = \
+  multidomainassembler.hh \
+  multidomainmodel.hh \
+  multidomainproperties.hh \
+  splitandmerge.hh \
+  multidomainconvergencewriter.hh \
+  multidomainnewtoncontroller.hh \
+  multidomainpropertydefaults.hh \
+  subdomainproperties.hh \
+  multidomainlocaloperator.hh \
+  multidomainproblem.hh \
+  pdelablocaloperator.hh \
+  subdomainpropertydefaults.hh
+endif
+
 include $(top_srcdir)/am/global-rules
diff --git a/dumux/multidomain/couplinglocalresiduals/Makefile.am b/dumux/multidomain/couplinglocalresiduals/Makefile.am
index 9e02ea7ece61d2111c2f16c3e6c7c711946f70a3..ba47b957357a64085d717b002ff5447f26bf53aa 100644
--- a/dumux/multidomain/couplinglocalresiduals/Makefile.am
+++ b/dumux/multidomain/couplinglocalresiduals/Makefile.am
@@ -1,4 +1,13 @@
 couplinglocalresidualsdir = $(includedir)/dumux/multidomain/couplinglocalresiduals
 couplinglocalresiduals_HEADERS = *.hh
 
+if !HAVE_DUNE_MULTIDOMAIN
+headercheck_IGNORE = \
+  2p2ccouplinglocalresidual.hh \
+  boxcouplinglocalresidual.hh \
+  stokesncnicouplinglocalresidual.hh \
+  2p2cnicouplinglocalresidual.hh \
+  stokesnccouplinglocalresidual.hh
+endif
+
 include $(top_srcdir)/am/global-rules
diff --git a/test/multidomain/2cnistokes2p2cni/Makefile.am b/test/multidomain/2cnistokes2p2cni/Makefile.am
index e6520df3f315a3c3951992ce643310c53d67ecb2..7be7032d4872c893eb8c6fc41bc9188697d3275c 100644
--- a/test/multidomain/2cnistokes2p2cni/Makefile.am
+++ b/test/multidomain/2cnistokes2p2cni/Makefile.am
@@ -1,5 +1,13 @@
-# tests where program to build and program to run are equal
+if HAVE_DUNE_MULTIDOMAIN
 check_PROGRAMS = test_2cnistokes2p2cni
+else
+headercheck_IGNORE = \
+  2cnistokes2p2cniproblem.hh \
+  2cnistokes2p2cnispatialparams.hh \
+  2p2cnisubproblem.hh \
+  stokes2cnisubproblem.hh
+endif
+
 test_2cnistokes2p2cni_SOURCES = test_2cnistokes2p2cni.cc
 
 include $(top_srcdir)/am/global-rules
diff --git a/test/multidomain/2cstokes2p2c/Makefile.am b/test/multidomain/2cstokes2p2c/Makefile.am
index ac442bfc93619b542a500dc69388eb0d3d108f72..520fb1d54ba205161b40c1f04acef539b7be59f0 100644
--- a/test/multidomain/2cstokes2p2c/Makefile.am
+++ b/test/multidomain/2cstokes2p2c/Makefile.am
@@ -1,5 +1,13 @@
-# tests where program to build and program to run are equal
+if HAVE_DUNE_MULTIDOMAIN
 check_PROGRAMS = test_2cstokes2p2c
+else
+headercheck_IGNORE = \
+  2cstokes2p2cproblem.hh \
+  2cstokes2p2cspatialparams.hh \
+  2p2csubproblem.hh \
+  stokes2csubproblem.hh
+endif
+
 test_2cstokes2p2c_SOURCES = test_2cstokes2p2c.cc
 
 include $(top_srcdir)/am/global-rules