More than 90% of congenital adrenal hyperplasia cases are caused by mutation of the CYP21A2 gene which converted from the CYP21A1P pseudogene. Sizes of the 3.7-kb TaqI-produced fragment that exists downstream of the TNXB gene, representing the CYP21A2, and the 3.2-kb TaqI-produced fragment that exists downstream of the XA gene, representing the CYP21A1P pseudogene, are used as size markers in the restriction fragment length polymorphism (RFLP) analysis. However, the size of and location for distinguishing these two genes might not be completely precise or reliable. Recent studies indicated that the 3.2-kb TaqI fragment may include multiple variants of chimeric CYP21A1P/CYP21A2 genes, a haplotype with dual mutations of IVS2-12A/C>G and 707-714del, and a functional CYP21A2 gene caused by small-scale conversions of the 5' end of the CYP21A1P sequence. In addition, a 3.7-kb TaqI fragment with more than 4 haplotypes of CYP21A2-like downstream of the TNXA gene and a 6.2-kb TaqI fragment of the CYP21A2 that results from a nucleotide mutation in the 3' end sequence were also identified. Accordingly, these structural variants reveal that traditional recognition of these two genes based on the TaqI fragment size analysis may lead to misinterpretation and increasingly interfere with the molecular diagnosis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency.