Lysosomal storage diseases (LSDs) are caused by enzyme deficiency in the cellular lysosomal apparatus, leading to a pathological accumulation of undigested cellular material (proteins, lipids or carbohydrates) and eventual tissue damage. Clinically and etiologically diverse, this group includes over 70 presently recognized hereditary conditions that have no effective therapy known to date. Most common manifestations of LSDs are brain lesions leading to various neurological deficits. Thus, the search for therapeutic strategies targeting these disorders represents an urgent unmet biomedical task, also necessitating the use of appropriate and valid experimental (animal) models. Here, we discuss the available models of LSDs and the applicability of rodents and zebrafish as model organisms for probing these pathologies.