Homeobox (HOX) genes encode a number of transcription factors, expressed along the developmental axis of the female genital tract during the embryonic period. Because HOX A10 and HOX A11 genes are expressed in the embryonic paramesonephric (Müllerian) ducts, abnormally low expression by mutant HOX A10 and HOX A11 genes might cause genital tract anomalies. This case-control study examined if one or more mutations in the HOX A10 and HOX A11 genes are included in the pathogenesis of the female genital tract anomalies. Blood samples were obtained from 30 women diagnosed with malformations of the genital tract (18 with septate uterus, three with bicornuate uterus, two with didelphys uterus, two with unicornuate uterus and five with aplasia/dysplasia) and 100 normal controls. DNA samples prepared from blood leukocytes were used as templates for polymerase chain reaction amplification of DNA fragments from HOX A10 and HOX A11 genes. The gene fragments were tested for DNA sequence differences using single-strand conformation polymorphism analysis and sequenced when genetic variation was detected. No subject showed a plausible causative mutation in HOX A10 or HOX A11; the sole variant observed (P38R) found in a patient with septate uterus was also present in her clinically normal mother.