Summary: We have developed a strategy to individually analyse large numbers of small tissue samples by RNA in situ hybridisation. Samples of approximately 0.4 mm × 0.5 mm are processed in rectangular capillary tubes fitted with nylon mesh and glass beads using standard protocols. Eighteen samples can be assayed simultaneously without loss, and background is low. Specifically, mouse Sox2 RNA expression is examined in the chorion of extraembryonic tissue of 7.5 days post‐coitum embryos. This technique works equally well for double RNA labelling and could potentially be used for antibody staining of proteins. genesis 27:76–80, 2000. © 2000 Wiley‐Liss, Inc.