Lysosomal neuraminidase 1 is responsible for sialic acid removal from oligosaccharides and glycoconjugates. Neu1 sialidase forms enzyme complex with protective protein cathepsin A, and glycosidase β-galactosidase. Mutations in Neu1 sialidase cause sialidosis, and Neu1-/- mice show symptoms of sialidosis patients. GM3 ganglioside is defined as substrate of lysosomal sialidase in vitro, and marked increase in GM3, GD3, and GM4 ganglioside levels in brain, spleen and liver autopsy tissues of sialidosis patients. Additionally, it was monitored that Neu1 has regulatory roles in immune response; expression of interleukins, activation of Toll-like receptor, and production of NF-kB in immune cells. However, relationship between inflammatory pathways and secondary lipid metabolisms in Neu1 sialidase deficiency remains unclear. Here, we aimed to investigate secondary lipid alterations and inflammatory response in tissues of Neu1-/- mice. In this study, lipidomic, molecular, histological and immunohistochemical analyses were performed in brain, spleen and kidney tissues of 2- and 5-month-old Neu1-/- mice. Decreasing levels of secondary lipids (phosphotidylcholine, phosphatidylethanolamine, and phosphotidylinositol) and elevated levels of pro-inflammatory cytokines, glycoconjugate accumulations, morphological degenerations, oligodendrocyte and neuronal loss, astrogliosis, and microgliosis were observed in brain, spleen and kidney of 2- and 5-month-old Neu1-/- mice. In the light of our findings, reduced levels of glycerophospholipids may be considered as biomarkers of activated inflammatory response in Type II sialidosis mice model. In the future studies, novel therapeutic strategies can target these altered glycerophospholipids, and their regulation can be crucial for alleviation of pathogenesis in sialidosis patients.