Genetics of human lysosomal arylsulfatases A and B (aryl-sulfate sulfohydrolase, EC 3.1.6.1), associated with childhood disease, has been studied with human-rodent somatic cell hybrids. Deficiency of arylsulfatase A (ARS(A)) in humans results in a progressive neurodegenerative disease, metachromatic leukodystrophy. Deficiency of arylsulfatase B (ARS(B)) is associated with skeletal and growth malformations, termed the Maroteaux-Lamy syndrome. Simultaneous deficiency of both enzymes is associated with the multiple sulfatase deficiency disease, suggesting a common relationship for ARS(A) and ARS(B). The genetic and structural relationships of human ARS(A) and ARS(B) have been determined by the use of human-Chinese hamster somatic cell hybrids. Independent enzyme segregation in cell hybrids demonstrated different chromosome assignments for the structural genes, ARS(A) and ARS(B), coding for the two lysosomal enzymes. ARS(A) activity showed concordant segregation with mitochondrial aconitase encoded by a gene assigned to chromosome 22. ARS(B) segregated with beta-hexosaminidase B encoded by a gene assigned to chromosome 5. These assignments were confirmed by chromosome analyses. The subunit structures of ARS(A) and ARS(B) were determined by their electrophoretic patterns in cell hybrids; a dimeric structure was demonstrated for ARS(A) and a monomeric structure for ARS(B). Although the multiple sulfatase deficiency disorder suggests a shared relationship between ARS(A) and ARS(B), independent segregation of these enzymes in cell hybrids did not support a common polypeptide subunit or structural gene assignment. The evidence demonstrates the assignment of ARS(A) to chromosome 22 and ARS(B) to chromosome 5. A third gene that affects ARS(A) and ARS(B) activity is suggested by the multiple sulfatase deficiency disorder.