We have used in situ hybridization techniques to describe the cellular distribution of transcripts from a Drosophila gene that encodes multiple FMRFamide-related neuropeptides. The Drosophila FMRFamide gene consists of two exons and is expressed predominantly as a approximately 1.7 kb RNA throughout postembryonic stages (Nambu et al., '88; Schneider and Taghert, '88, '90). We used exon-specific oligonucleotide probes to assay transcription in both embryonic and larval stages and found a pattern of hybridization signals that was restricted to the central nervous system and, within that tissue, was cell-specific. The pattern included 36 distinct signals distributed throughout both the brain and segmental nerve cord (ventral ganglion). These observations suggest that the cell-specific pattern of FMRFamide-like neuropeptide expression in the Drosophila CNS (White et al., '86; Taghert and Schneider, '90) is due to the restricted expression of specific gene transcripts. The results also indicate that, with few exceptions, all previously identified FMRFamide-immunoreactive neurons in Drosophila larvae express FMRFamide gene transcripts. The 36 hybridization regions of the CNS could be divided into three categories, based on their signal intensities (strong, moderate, and weak). The differences in intensity were reproducible and suggest that steady-state levels of specific neuropeptide RNA differ among individual neurons. The two exon-specific probes produced patterns that were indistinguishable both in pattern and in intensity. This result supports the previous conclusion that the one detectable FMRFamide transcript contains both exons (Schneider and Taghert, '90). A single identifiable signal was detected during embryogenesis (beginning at stage 16), but the mature complement of signals was not fully established until the final larval stages.