Niemann–Pick type C disease (NPC), a neurovisceral disorder characterized by accumulation of unesterified cholesterol and glycolipids in the lysosomal/late endosomal system, is due to mutations on either the NPC1 or the NPC2 genes. We report the diagnosis of six unrelated patients with NPC2, all with homozygous mutations. We further attempted functional characterization of the p.P120S, p.Q146X and IVS1 + 2 t>c mutations under native conditions. This was achieved by immunoblotting and immunocytofluorescence microscopy on cultured skin fibroblasts and in silico modeling. IVS1 + 2 t>c led to multiple transcripts, with only abnormally spliced cDNAs. Among the three NPC2 variants, only p.P120S led to detectable amounts of an immunoreactive protein. This protein showed a normal lysosomal localization. Our results suggest that the p.P120S mutation, the first naturally occurring missense mutation located in the cholesterol-binding Evolutionarily Constrained Regions D domain, results in reduced amounts of a protein capable to reach the lysosome, but unable to efficiently bind cholesterol. The patient had a juvenile neurological onset form of the disease. An update of the 22 families with mutations in the NPC2 gene, currently known to us, confirms the good genotype–phenotype correlations seen in this disorder. Characterization of more naturally occurring NPC2 mutations may help to dissect further the functional domains of the protein.