ABSTRACT Mutations in either ClC‐7, a late endoso‐ mal/lysosomal member of the CLC family of chloride channels and transporters, or in its β‐subunit Ostm1 cause osteopetrosis and lysosomal storage disease in mice and humans. The severe phenotype of mice globally deleted for ClC‐7 or Ostm1 and the absence of storage material in cultured cells hampered investiga‐ tions of the mechanism leading to lysosomal pathology in the absence of functional ClC‐7/Ostm1 transporters. Tissue‐specific ClC‐7‐knockout mice now reveal that accumulation of storage material occurs cell‐autono‐ mously in neurons or renal proximal tubular cells lacking ClC‐7. Almost all ClC‐7‐deficient neurons die. The activation of glia is restricted to brain regions where ClC‐7 has been inactivated. The effect of ClC‐7 disruption on lysosomal function was investigated in renal proximal tubular cells, which display high endo‐ cytotic activity. Pulse‐chase endocytosis experiments in vivo with mice carrying chimeric deletion of ClC‐7 in proximal tubules allowed a direct comparison of the handling of endocytosed protein between cells express‐ ing or lacking ClC‐7. Whereas protein was endocytosed similarly in cells of either genotype, its half‐life in‐ creased significantly in ClC‐7‐deficient cells. These ex‐ periments demonstrate that lysosomal pathology is a cell‐autonomous consequence of ClC‐7 disruption and that ClC‐7 is important for lysosomal protein degrada‐ tion.—Wartosch, L., Fuhrmann, J. C., Schweizer, M., Stauber, T., Jentsch, T. J. Lysosomal degradation of endocytosed proteins depends on the chloride trans‐ port protein ClC‐7. FASEB J. 23, 4056 – 4068 (2009). www.fasebj.org