Steroid 21-hydroxylase deficiency is the major cause of congenital adrenal hyperplasia. Genotyping for deletions and nine point mutations in the CYP21 gene has been performed in 38 Spanish patients and their relatives by Southern blot analysis and allele-specific oligonucleotide hybridization. Three clinical variants were included in this study, viz., salt-wasting (SW, 21 patients), simple virilizer (SV, two patients), and late-onset (LO, 15 patients) forms. Twenty-three patient genotypes (16 SW, two SV, and five LO) were fully characterized. In both alleles, all but one of these severe forms (SW and SV) presented mutations that abolished or severely affected enzymatic activity. Patients with LO forms showed mutations that moderately impaired enzymatic activity in both alleles, or severe mutations in only one chromosome. Of 46 chromosomes from severe forms, 41 were characterized in this study (89%). The most frequent mutation was an aberrant splicing site (655 A or C to G) in intron 2, in 30% of these chromosomes. Deletions were found in 20%, and large gene conversions in 13% of these alleles. This screening allowed the characterization of 18 out of 30 LO chromosomes, the most frequent mutation being Val281Leu (37%). Severe mutations were found, in heterozygosis, in one third of LO patients.