Most cases (90%) of congenital adrenal hyperplasia (CAH) are secondary to steroid 21-hydroxylase enzyme deficiency (P450c21). In human, the P450c21 gene (CYP21B) is present along with a non functional pseudogene (CYP21A). These genes, located in chromosome 6, present a sequence homology of 98%. This high homology and the complexity of this gene locus brings about considerable difficulties in its molecular analysis and in the interpretation of the results. The aim of the present study was to elaborate an adequate strategy for the analysis of the most frequent mutations described in the CYP21B gene. A total of 77 patients with clinical and biochemical diagnosis of CAH secondary to P450c21 enzyme deficiency, as well as 170 unaffected relatives, were studied. They belonged to 73 unrelated families (146 chromosomes). The strategy allowed for the differentiation of patients with homozygous point mutations (PM), with PM in one allele and deletions, conversions, Ex3 or Cluster Ex6 PM in the other, even though parents were not always available for the study. Furthermore, it allowed for the discrimination of heterozygous deletions or conversions of the CYP21B gene from duplications of the non functional gene CYP21A, as well as CYP21B and A deletions from normal copies of the two genes. An exhaustive molecular analysis of this gene is necessary for an adequate characterization of the alterations present in this locus.