Sanfilippo syndrome type A (mucopolysaccharidosis type IIIA; MPS IIIA) is caused by a deficiency of the lysosomal enzyme haparan N-sulphatase (NS). The genomic DNA segments of the NS gene from two Chinese patients with MPS IIIA were amplified by polymerase chain reaction, followed by DNA sequencing to study the molecular lesions. Four mutations (i.e. N42K, D235N, P293S and R377C) and five polymorphisms (i.e. IVS2-72A --> G, IVS2-26T --> C, IVS5+17C --> T, IVS5-37GC --> CTGT and R456H) were identified. Transfection of COS-7 cells with cDNA mutagenized to the corresponding mutations did not yield active enzyme, demonstrating the deleterious nature of the mutations. Western blot analysis revealed a 62-kDa precursor and 56-kDa mature forms for cells transfected with wild-type and polymorphic R456H enzymes. For cells transfected with mutant enzymes, the reduction in precursor and mature forms suggests an increased degradation of the mutant enzymes. The polymorphic DNA haplotype of the NS gene was analysed in 52 unrelated subjects. All five polymorphisms were in Hardy-Weinberg equilibrium. The strong non-random association among the five polymorphisms suggests little or no recombination in the NS gene.