Gaucher disease is caused by the inherited deficiency of the enzyme glucocerebrosidase (EC 3.2.1.45). The gene for glucocerebrosidase is located on chromosome 1q21 and a highly homologous pseudogene is situated 16kb downstream. Two novel polymorphisms were identified in the glucocerebrosidase gene region: the first consists of a variable number of tetranucleotide (AAAT) repeats located upstream of the glucocerebrosidase gene, and the second is a series of dinucleotide (CT) repeats found in the intergenic region between the glucocerebrosidase gene and its pseudogene. These two polymorphisms, along with the previously reported PvuII polymorphism in intron 6 of the glucocerebrosidase gene, were analyzed in an affected population (n=102) and in two normal control populations, one consisting of non-Jewish individuals of mixed ethnic background (n=46) and the second of Ashkenazi Jewish individuals(n=72). Strong linkage disequilibrium was found between mutations N370S, 84GG, and R463C and specific haplotypes; no significant linkage disequilibrium was found in patients carrying mutation L444P. Unexpected haplotypes lead to the recognition of several genotyping errors and complex alleles. These two novel polymorphic sites provide a new tool for the identification of mutant alleles in patients and for the study of founder effects in populations with Gaucher disease.