The Niemann-Pick-type C1 (Npc1) protein mobilizes LDL-derived cholesterol from lysosomes. Npc1 deficiency disease is a panethnic autosomal recessive disorder of intracellular cholesterol trafficking, leading to accumulation of cholesterol in endosomes/lysosomes. This report assesses the effects of a spontaneous inactivating mutation of the Npc1 gene on spermatogenesis and cholesterol homeostasis in mice. We quantified 1) free and esterified cholesterol levels by enzymatic analysis, 2) cholesterol enzymes and transporter protein expression by Western blotting, and 3) the number of Apostain-labeled apoptotic germ cells and apoptosis levels by ELISA in seminiferous tubule-enriched fractions. In wild-type (WT) mice, esterified cholesterol was elevated when Npc1 expression was low during puberty, while in adulthood, the levels were low (P < 0.05) when Npc1 expression was high (P < 0.01). In Npc1−/− mice, free and esterified cholesterol were significantly elevated. The abundance of cholesterol regulatory proteins, HMGR ACAT1, ACAT2, SR-BI, and ABCA1 was significantly higher in Npc1−/− than in WT mice. The level of apoptosis determined by ELISA and the number of Apostain-labeled cells/tubule were higher in Npc1−/− than in WT mice. Circulating testosterone levels in the Npc1−/− males were threefold lower than those observed in the WT. Deleting the Npc1 gene is accompanied by an increase in germ cell apoptosis and compensatory imbalances in the expression of cholesterol enzymatic and transporter factors and is associated with esterified cholesterol accumulation in seminiferous tubules.