The relative rarity of human lysosomal disorders, extremely heterogeneous genetic background and ethical restrictions make well-controlled studies difficult with human patients. Genetically authentic animal models complement human patients with their ready availability, homogeneous genetic background and the relatively flexible experimental designs. Spontaneous animal models of human lysosomal disorders are rare, particularly among small laboratory animals. However, the homologous recombination and embryonic stem cell technology has so far enabled us to duplicate almost all known human sphingolipidoses, two mucopolysaccharidoses and aspartylgly-cosaminuria in mice and more disorders are expected in the near future. This technology also allows generation of mouse mutants that are not known or are highly unlikely to exist in humans, such as 'double-knockouts'. Studies of lysosomal disease have come to the half-way turning point of the marathon race from clincopathological descriptions, identification of affected compounds, enzymology, to the present gene-level inquiries. The animal models will play an important role in our long journey from nucleic acids back to biology. While the utility of these mouse models is obvious, species differences in the brain development and metabolic pathways must be always remembered if the ultimate goal of the study is application to human patients. After all, the mouse is not human.