A diagnosis of a mucopolysaccharidosis disorder is made based upon a thorough clinical evaluation, identification of characteristic findings (e.g., coarse facial features, skeletal malformations, hepatosplenomegaly), and a variety of specialized tests including urine analysis to detect excessive levels of mucopolysaccharides. Tests known as enzyme assays may be performed to detect deficient levels of lysosomal enzymes in cells of the body.

Newborn screening for MPS I has recently been approved for inclusion in the Recommended Universal Screening Panel, although each state decides independently when or if, it will be added to its newborn screening panel MPS II is currently being screened in Illinois. After an abnormal newborn screening result, it would be necessary to follow up with a definitive diagnosis by enzyme assay.

Prenatal diagnosis is possible through the use of amniocentesis and chorionic villus sampling. During amniocentesis, a sample of fluid that surrounds the developing fetus is removed and studied. During CVS, tissue samples are removed from a portion of the placenta and DNA studies may be performed, primarily in families with a previously affected child, and the abnormal gene mutations are known.