Mucopolysaccharidosis IIID (MPSIIID) is an inherited lysosomal storage disease resulting from lack of the activity of the N-acetylglucosamine-6-sulfatase, which is one of the enzymes involved in the step-wise degradation of heparan sulfate. MPS IIID in goats has been described and characterized. Goats with this disorder demonstrate delayed motor development and growth retardation. Even if they reach sexual maturity, they will suddenly die from congestive heart failure. A molecular base for this disorder is a nonsense mutation at nucleotide 322 (C→T) results in the change of the arginine codon to a stop codon, which leads to stop enzyme function. However, this also creates a recognition site for AluI restriction enzyme for a genetic analysis. The aim of this study is to detect the presence of MPS IIID genetic disorder in Turkish native goat breeds. A total of 120 blood samples from 13 different native goat breeds were used as a material. Polymerase chain reaction (PCR) - Restriction fragment length polymorphism (RFLP) and DNA sequence data were utilized to identify the goat populations. The result of this study indicates nonsense mutation that causes MPS IIID genetic disorder is found in none of Turkish Native Goat breeds. However, a silent mutation was found at nucleotide 354 (T→C) when compared with reference sequence.