Tight regulation of retinoic acid (RA) distribution in the embryo is critical for normal morphogenesis. The RA-metabolizing enzymes Cyp26A1 and Cyp26B1 are believed to play important roles in protecting certain embryonic tissues from inappropriate RA signaling. We have cloned the murine Cyp26B1 cDNA and compared its expression pattern to that of Cyp26A1 from embryonic day (E) E7-E11.5 using in situ hybridization. Northern blot analysis shows the presence of two Cyp26B1 transcripts of approximately 2.3 and 3.5 kb in embryonic limb bud. Whereas Cyp26A1 is expressed in gastrulating embryos by E7, Cyp26B1 is first expressed at E8.0 in prospective rhombomeres 3 and 5. Cyp26B1 expression expands to specific dorso-ventral locations in rhombomeres 2-6 between E8.5 and E9.5, whereas Cyp26A1 hindbrain expression is limited to rhombomere 2 at E8.5. No (or very weak) Cyp26B1 expression is observed in the tail bud, a major site of Cyp26A1 expression. Differential expression is seen in branchial arches, with Cyp26A1 being mainly expressed in neural crest-derived mesenchyme, and Cyp26B1 in specific ectodermal and endodermal areas. Cyp26B1 is markedly expressed in the ectoderm and distal mesoderm of the limb buds from the beginning of their outgrowth. Cyp26A1 transcripts are seen later and at lower levels in limb ectoderm, and both transcripts are excluded from the apical ectodermal ridge.