Prolidase (E.C.3.4.13.9) is a homodimeric enzyme encoded at a locus on chromosome 19. Prolidase deficiency is an autosomal recessive disorder with a highly variable clinical phenotype. We purified prolidase to homogeneity from normal human fibroblasts, raised a monospecific rabbit antiserum, and studied biosynthesis of the subunit in normal and prolidase--deficient fibroblasts. Pulse-chase immunoprecipitation experiments showed that the subunit is synthesized and retained in cytosol as a 58-KDa polypeptide. Three types of mutations were identified in six prolidase-deficient cell strains; half conferred a CRM-negative phenotype, while the CRM-positive mutations were of two types, one mutation encoding an enlarged subunit (60 KDa) and the others associated with subunits of normal size. Complementation analysis indicated that these mutations map to one locus. Normal subjects and obligate heterozygotes expressing CRM-negative mutations had thermostable prolidase activity at 50 degrees C in cell extracts, whereas heterozygotes expressing CRM-positive mutations had thermolabile activity under the same condition, implying negative allelic complementation in the putative heterodimer. The occurrence of prolidase-like activity about 5% of normal in amount but with a preference for substrate different from normal, in cells homozygous (or compound) for CRM-negative mutations, identified an alternative cleavage activity not encoded at the prolidase locus. Allelic heterogeneity at the major locus and the amount of alternative peptidase activity encoded elsewhere appear to be determinants of the associated and heterogeneous clinical phenotype.