For investigating the possible influence of maternal-fetal HLA compatibility on maternal microchimerism, DNA samples from blood of 120 maternal-fetal pairs were genotyped at two polymorphic loci: glutathione-S-transferase M1 (GSTM1) and angiotensin-converting enzyme (ACE). Informative pairs (mother heterozygous/fetus homozygous at one of the two loci) were then tested by quantitative real-time PCR for the noninherited maternal allele (s) and genotyped at the HLA-A, B, and C class I loci and/or at the DRB1 and/or DQB1 class II loci. Small numbers of maternal cells were detected in the circulation of 16 of the 30 informative second-and third-trimester fetuses. Comparison with HLA data suggested an association between microchimerism and maternal compatibility at the class II DRB1 and/or DQB1 HLA loci and with the maternal HLA-DQB1* 0301 allele. There was no relationship between maternal microchimerism and maternal-fetal HLA compatibility at other HLA loci or with gestational age, fetal anomalies, or red cell or platelet isoimmunity.