Alternative splicing of eukaryotic messenger RNA precursors represents a common mechanism for generating multiple transcripts from a single gene. Although there has been increasing information concerning the sequence requirements and the biochemical mechanisms involved in the constitutive splicing of primary RNA transcripts, very little is known about the sequences or mechanisms which determine alternative RNA-processing events in complex transcription units. The calcitonin/calcitonin gene-related peptide (CGRP) primary RNA transcript undergoes tissue-specific alternative processing, resulting in the differential production of calcitonin mRNA in thyroid C cells and CGRP mRNA in neurons of the central and peripheral nervous systems. To elucidate the molecular mechanisms underlying these alternative RNA processing events, we have examined the nucleotide sequences involved in the production of calcitonin and CGRP mRNAs. Analyses of HeLa and F9 cell lines transfected with a variety of mutant calcitonin/CGRP transcription units have demonstrated that alternative splice-site selection is primarily regulated by cis-active element(s) near the calcitonin-specific 3'-splice junction. We suggest that the tissue-specific pattern of alternative RNA processing is conferred by sequence information at the calcitonin-specific acceptor which serves to inhibit the production of calcitonin transcripts in CGRP-producing cells.