Gaucher disease (GD) is the most frequent lysosomal storage disease, caused by mutations in the acid beta-glucosidase gene (GBA). The c.1226A > G (N370S) mutation is associated with non-neuronopathic disease (type 1). However, we have observed some discrepancy between genotype and phenotype in Spanish Gaucher disease patients homozygous for the c.1226A > G mutation. A deletion of 55 bp in the exon 9 GBA gene, corresponding to the deleted portion of the beta-glucosidase pseudogene, has been previously reported as a cause of erroneous assignment of 1226G/1226G homozygous patients when the genotype has been performed by PCR assay. We had originally identified 25 (out of 124) unrelated Gaucher disease patients as being putative homozygotes for the c.1226A > G mutation. By means of a new PCR-based assay, we were able to distinguish between the true homozygous patients and the carriers of the 55-bp deletion in exon 9 of the GBA gene. The 55-bp deletion was detected in 10 out of 25 samples (40%) [7 with the 55-bp deletion, 1 RecTL, 1 RecNciI (both including the deletion) and one rearrangement]. Such a high prevalence in this sample suggests that this allele can be more common than expected among GD patients.