The diversity of the genes encoding mammalian proteoglycan peptide cores was explored using a cDNA clone that encodes the partial sequence of a cell surface/pericellular matrix-localized chondroitin sulfate proteoglycan. Thus we were able to detect the expression of the gene(s) encoding the intracellular chondroitin sulfate proteoglycan produced by a variety of rat and mouse mucosal-like mast cells and the intracellular heparin proteoglycan synthesized by rat serosal mast cells. The cDNA from the proteoglycan cDNA clone pPG-1 was fractionated into two discrete fragments, one of which contained the nucleotides encoding the serine-glycine repeat sequence (pPG-B) and the other of which contained sequences on the 3' side of the repeat (pPG-M). As assessed by Southern blot analysis, pPG-B identified a large gene family, whereas pPG-M identified a single DNA fragment in the rat genome. When the pPG-1 insert and the two subcloned probes pPG-B and pPG-M were used to analyze RNA extracted from the rat and mouse mucosal-like mast cells and the rat serosal mast cells, the same major RNA species was detected at 1.3 kilobases with both probes. These data suggest that the gene responsible for the peptide core of the extracellular chondroitin sulfate proteoglycan synthesized by the rat yolk sac cell line is also the gene that encodes the core peptides of the secretory granule-localized chondroitin sulfate and heparin proteoglycans.