AbstractA healthy female with a brother suffering from Lesch–Nyhan syndrome was assigned a carrier status on the basis of haplotype analysis employing flanking and intragenic polymorphic markers of the HPRT gene. Her mother has been confirmed as a definite carrier by cell growth selection studies in cultured fibroblasts. In our proposita's first pregnancy, a male fetus was identified carrying the risk allele. Afterwards, the underlying novel mutation A161E (GCA→GAA at position c482) could be identified in the affected brother and in the heterozygous mother but not in the DNA of the pregnant sister and fetus. The fetus was also confirmed to be normal by uptake of 14C‐hypoxanthine in cultured amniotic cells. To test the discrepancy, the investigation was extended by recruiting additional family members. The data obtained showed that the mother had passed her risk haplotype to the affected son as well as to her mutation‐carrying and non–mutation‐carrying daughters. This provides the first evidence of concomitant somatic and germline mosaicism in Lesch–Nyhan syndrome. The study has a bearing on genetic counselling and cautions against the reliability of only using indirect genetic diagnosis even with intragenic markers. Copyright © 2004 John Wiley & Sons, Ltd.