Tissue differentiation during embryonic development involves activation of specific genes. To isolate genes selectively expressed in mesoderm and nervous system in the Drosophila embryo, we have screened a cDNA library with molecular probes enriched in specific gene sequences from both tissues. In this way, we have isolated six mesoderm-specific genes, as demonstrated by in situ hybridization to embryo sections. Two of these genes, expressed during muscle differentiation, are described here for the first time. These genes have been localized in the 17A region of the first chromosome and in the 60A region of the second chromosome, respectively. No neural-specific genes were identified using this approach, most probably because of the low sensitivity of detection methods which combine filter hybridization techniques with the use of complex probes.