Objective: Mucopolysaccharidoses is a group of inherited lysosomal storage diseases that are manifested by various clinical signs and symptoms (skeletal dysplasia, coarse face, progressive psychomotor retardation, cardiac and lung involvement) due to the deposition of glycosaminoglycans in tissues. Recently it has been shown that the inflammatory response to glycosaminoglycan deposition in leucocytes in animal models of mucopolysaccaridoses has increased. Here, we aimed to investigate some inflammatory markers (galectin-3, cathepsin-D and chitotriosidase) as diagnostic markers in different types of mucopolysaccharidosis and in patients with Gaucher disease and Niemann Pick A/B disease. Methods: Plasma samples were collected from patients with mucopolysaccharidosis (n=25), Gaucher Disease (n=16), Niemann Pick A/B (n=5) and 15 healthy controls. All subjects were under the age of 18 years. Chitotriosidase enzyme activities were determined fluorometrically, cathepsin-D and galectin-3 levels were determined by using the ELISA kit. Results: Chitotriosidase enzyme activities were statistically significantly higher in patients with MPS IV than the control group. Cathepsin-D levels were higher in patients with MPS I, MPS III and MPS IV, galectin-3 levels were higher in patients with MPS I, MPS IV and MPS VI when compared to healthy controls. All three parameters were higher in patients with Gaucher disease and Niemann Pick A/B disease. Conclusion: Elevated levels of galectin-3 in MPS I, MPS IV and MPS VI and elevated levels of cathepsin-D in MPS I, MPS III and MPS VI support the influence of inflammatory process in the pathophysiology of mucopolysaccharidosis and might be promising new biomarkers in the diagnosis with high sensitivity and specificity.