Stripe rust resistance in the winter wheat cultivar Claire has remained effective in the UK and Europe since its release in 1999. To characterise this valuable source of resistance a cross was made between Claire and the stripe rust susceptible cultivar Lemhi, producing F2:3 and doubled haploid (DH) populations. A genetic linkage map was constructed using SSR, AFLP, DArT and NBS-AFLP markers that had a total map length of 1730 cM. To improve the definition of the two QTL identified on the long arm of chromosome 2D EST-derived markers were developed from EST mapped to the 2D terminal deletion bin, 2DL 0.76-1.00. Stripe rust resistance was evaluated on adult plants under field and glasshouse conditions by measuring the extent of fungal growth, Percentage infection (Pi) and the necrotic/chlorotic response of the plant to infection, Infection Type (IT). Four QTL contributing to stripe rust resistance were identified in Claire, QPst.claire-2Da, QPst.claire-2Db, QPst.claire-2B, and QPst.claire-7B. For the Pi phenotype QPst.claire-2Da explained up to 25.4% of the phenotypic variation, QPst.claire-2Db up to 28.7%, QPst.claire-2B up to21.7% and QPst.claire-7B up to 13.0%. For IT the percentages of the phenotypic variation explained were 23.4%, 31.8%, 17.2% and 12.6%, respectively. Examination of DH lines carrying QPst.claire-2Db identified variation in the Pi phenotype, lines either showing a highly resistant phenotype or an intermediate resistant Pi value. This led the authors to propose the possibility of a suppressor, originating from Lemhi that acted specifically towards the QTL QPst.claire-2Db. In addition to the four QTL conferring stripe rust adult plant resistance (APR) in Claire, a race-specific, seedling expressed resistance gene was identified on chromosome 3B which is no longer effective against UK pathotypes of the stripe rust fungus Puccinia striiformis f. sp. tritici.