Arylsulfatase A (ASA) is a lysosomal enzyme that hydrolyzes sulfatide. Absence of ASA activity leads to metachromatic leukodystrophy (MLD). The clinical outcome resulting from ASA deficiency is highly variable with respect to age of onset and symptoms. So far the causes for the variability are poorly understood. We have studied the relationship between the ASA genotype and the clinical phenotype. Fibroblasts from a total of 34 subjects with low ASA activity were examined with immunoblotting, a sensitive ASA assay, and the sulfatide loading test in order to characterize low ASA activity further. By these methods, three different classes of ASA deficiency can be defined: homozygosity for the pseudodeficiency allele (ASAp), compound heterozygosity for the ASAp and MLD (ASA-) alleles, and ASA-/ASA- genotypes. These genotypes exhibit different levels of ASA residual activity. Only ASA-/ASA- genotypes are associated with MLD. For diagnostic purposes, however, the differentiation of the various ASA genotypes is essential.