A metachromatic leukodystrophy (MLD) patient was found to carry two additional arylsulfatase A (ARSA) alleles besides the two inherited. The additional alleles arose from an event of mitotic intragenic recombination between the inherited alleles, thus leading to a case of somatic mosaicism. As suggested by in vitro expression, the recombination was ineffective in generating a significantly advantaged ARSA allele compared to the inherited alleles. Although the phenotype in this patient was not modified by the recombination, similar events could potentially yield significant clinical benefits.