Individuals with MPS disorders share many similar symptoms such as multiple organ involvement, distinctive "coarse" facial features, and abnormalities of the skeleton especially joint problems. Additional findings include short stature, heart abnormalities, breathing irregularities, liver and spleen enlargement (hepatosplenomegaly), and/or neurological abnormalities. The severity of the different MPS disorders varies greatly among affected individuals, even among those with the same type of MPS and even among individuals of the same family.

In most cases of MPS, affected infants appear normal at birth and symptoms become apparent around the age of one or two, however, in MPS VII, approximately 40% of pregnancies with an affected baby are complicated by a condition called non-immune hydrops fetalis that may be detected on routine ultrasound examination. Initial symptoms may include frequent colds, runny nose, infections, growth delays, or mild developmental delays. Mild forms of these disorders may not become apparent until childhood or adolescence. In most cases, the mucopolysaccharidoses are chronic, progressive disorders and, depending upon the type of MPS and severity, affected individuals may experience a decline in physical and mental function, sometimes resulting in life-threatening complications.