The purpose of the present study was to clarify roles of cytosolic chloride ion (Cl −) in regulation of lysosomal acidification [intra-lysosomal pH (pH lys)] and autophagy function in human gastric cancer cell line (MKN28). The MKN28 cells cultured under a low Cl − condition elevated pH lys and reduced the intra-lysosomal Cl − concentration ([Cl −] lys) via reduction of cytosolic Cl − concentration ([Cl −] c), showing abnormal accumulation of LC3II and p62 participating in autophagy function (dysfunction of autophagy) accompanied by inhibition of cell proliferation via G 0/G 1 arrest without induction of apoptosis. We also studied effects of direct modification of H + transport on lysosomal acidification and autophagy. Application of bafilomycin A1 (an inhibitor of V-type H +-ATPase) or ethyl isopropyl amiloride [EIPA; an inhibitor of Na +/H + exchanger (NHE)] elevated pH lys and decreased [Cl −] lys associated with inhibition of cell proliferation via induction of G 0/G 1 arrest similar to the culture under a low Cl − condition. However, unlike low Cl − condition, application of the compound, bafilomycin A1 or EIPA, induced apoptosis associated with increases in caspase 3 and 9 without large reduction in [Cl −] c compared with low Cl − condition. These observations suggest that the lowered [Cl −] c primarily causes dysfunction of autophagy without apoptosis via dysfunction of lysosome induced by disturbance of intra-lysosomal acidification. This is the first study showing that cytosolic Cl − is a key factor of lysosome acidification and autophagy.