The basilar pons, a major hindbrain nucleus involved in sensory-motor integration, has become a model system for studying long-distance neuronal migration, axon-target recognition by collateral branching, and the formation of patterned axonal projections. To identify genes potentially involved in these developmental events, we have performed a differential display PCR screen comparing RNA isolated from the developing basilar pons with RNA obtained from developing cerebellum and olfactory bulb, as well as the mature basilar pons. Using 400 different combinations of primers, we screened more than 11,000 labeled DNA fragments and identified 201 that exhibited higher expression in the basilar pons than in the control tissues. From these, 138 distinct gene fragments were cloned. The differential expression of a large subset of these fragments was confirmed using RNase protection assays. In situ hybridization analysis revealed that the expression of many of these genes is limited to the basilar pons and only a few other brain regions, suggesting that they may play specific roles in pontine development.