Rat mast cell granules contain a spectrum of enzymes as established by histochemical techniques and subcellular fractionation. However, 35% of the beta-glucuronidase, 30% of the beta-D-galactosidase, 14% of the beta-hexosaminidase and all of the acid phosphatase is not available for immunologic release from purified rat serosal mast cells, suggesting the presence of nonsecretory lysosomes containing these acid hydrolases. On the other hand, immunologic release of the majority of chymase, beta-hexosaminidase, beta-glucuronidase, beta-D-galactosidase, and arylsulfatase A occurs in parallel with histamine and thereby localizes these substances to the rat mast cell secretory granule. A molecular model of the secretory granule in the resting mast cell can now be constructed in which heparin proteoglycan is the granule matrix to which chymase and probably other proteins are ionically bound. Inhibition of chymase by serotonin stored in its active site and of chymase and acid hydrolases by their interaction with heparin probably occurs. Histamine is stored by ionic linkage to carboxyl groups of protein and heparin. Micromolar amounts of heparin glycosaminoglycans, histamine, serotonin, chymase, beta-D-hexosaminidase, beta-glucuronidase, and arylsulfatase A in secretory granules of 10(6) mast cells are 0.7--1.3 x 10(-3), 70--220 x 10(-3), 0.9--28 x 10(-3), 0.2--0.5 x 10(-3), 0.9--2.7 x 10(-6), 0.1--0.3 x 10(-6) and less than 8 x 10(-6), respectively. In addition, the total protein available for calcium ionophore-induced release from 10(6) rat mast cells is about 60 microgram, indicating that less than 50% of the granule protein can be accounted for. Recognition that mast cell secretory granules contain acid hydrolases indicates that they are modified lysosomes; their special intracellular and extracellular functions are dictated by the associated novel constituents and the stimulus for activation.