Congenital adrenal hyperplasia due to 21-hydroxylase deficiency is one of the most common inherited metabolic diseases. We studied 52 Japanese 21-hydroxylase deficiency patients corresponding to 49 families (98 chromosomes) to detect the mutations in 21-hydroxylase genes using Southern blotting, PCR-restriction fragment length polymorphism, and a direct sequencing method. Among the 52 patients (49 families), 35 patients (33 families) were diagnosed as the salt-wasting type, 12 (12 families) as the simple virilizing type, and 5 (4 families) as the nonclassical type. Our findings were as follows. 1) The complete genotype that had homozygous or compound heterozygous mutations was determined in 43 of 49 families (87.8%). Among the remaining patients, no mutation was found in the structural gene of either allele in 3 cases, and a mutation was detected in only 1 allele in 3 cases. This means that at least 9 of 98 alleles have some unusual mutations or recombinations that we cannot detect by our method or gene defects outside of the structural gene. 2) Although the common mutation of Caucasian nonclassical patients is V281L, none of our 4 nonclassical families showed this mutation, and 3 of them had the P30L mutation at least on 1 allele. 3) We identified a putative new mutation, homozygous deletion of adenine at codon 246, in a salt-wasting patient. Although we have not analyzed the functional consequence of this mutation, it causes substitution noncoding for Met(256) in exon 7 and premature termination of the mRNA before the heme-binding region of the P450 polypeptide, which would result in a completely nonfunctional enzyme.