Posttranslational processing of peptide precursors frequently includes COOH-terminal amidation by the bifunctional enzyme peptidylglycine alpha-amidating monooxygenase (PAM). We examined the ontogeny of PAM gene expression using in situ hybridization and detected expression in the cardiogenic region beginning at embryonic day 9 (e9) and in decidualizing uterine endometrium and myometrial smooth muscle at even earlier postimplantation stages. PAM expression in the CNS at e10 was highest in the dorsal spinal cord and floor plate and exhibited complex patterning in several CNS regions, including the ventricular zone, over the next several days with PAM expression first detected in neurons at e13. High levels of PAM expression characterized several nonneural cell populations as well, including limb mesoderm and the mesenchyme immediately adjacent to nasal, maxillary, palatal, and dental epithelia during tissue fusion and remodeling. Since alternative splicing generates PAM transcripts encoding proproteins that are differentially localized and processed, we used probes that distinguish major subsets of PAM transcripts to determine that transcripts encoding integral membrane PAM isoforms predominate in most, if not all, PAM-expressing cell types throughout development. Further, transcripts that encode soluble and cleavable PAM isoforms are essentially absent from two CNS areas that are rich in transcripts encoding integral membrane, bifunctional PAM: the ependymal region of the spinal cord and the ventricular zone of the hippocampus. These results provide evidence for widespread expression and cell-type-specific alternative splicing of PAM during development and raise the possibility that region-specific amidation of PAM substrates contributes significantly to several developmental processes.