Last data described that patients with lysosomal storage disorders (LSDs) may have clinical schizophrenia (SCZ). The lysosomal dysfunction in SCZ pathogenesis, in particularly, due to the critical role of lysosomal function for neuronal cells could be proposed. The current study focused on the estimation of lysosomal enzyme activities and alpha-synuclein level in blood cells of patients with late-onset SCZ. 52 SCZ patients with late-onset SCZ, 180 sporadic Parkinson’s disease (sPD) patients, 176 controls were recruited. The enzymatic activity of enzymes associated with mucopolysaccharidosis (alpha-L-Iduronidase (IDUA)), glycogenosis (acid alpha-glucosidase (GAA)) and sphingolipidosis (galactosylceramidase (GALC), glucocerebrosidase (GCase), alpha-galactosidase (GLA), acid sphingomyelinase (ASMase)) was measured by LC-MS/MS in blood. Alpha-synuclein level was estimated in magnetically separated CD45+ blood cells by the enzyme-linked immunosorbent assay (ELISA). NGS analysis of 11 LSDs genes was conducted in 21 early-onset SCZ patients and 23 controls using the gene panel PGRNseq-NDD. Decreased ASMase and increased GLA activities and increased alpha-synuclein level were observed in late-onset SCZ patients in comparison to controls (p<0.05). 4 rare deleterious variants among LSDs genes causing mucopolysaccharidosis type I (IDUA (rs532731688, rs74385837) and type III (HGSNAT (rs766835582)) and sphingolipidosis (metachromatic leukodystrophy (ARSA (rs201251634)) were identified in five patients from group of early-onset SCZ but not in controls. Our findings supported the role of sphingolipid metabolism in SCZ pathogenesis. Aberrant enzyme activities and compound of sphingolipids associated with ceramide metabolism may lead to accumulation of alpha-synuclein and be a critical in SCZ.