The AF1q gene is expressed in normal haematopoietic progenitors, but less so in differentiated blood cells. In 47 patients with myelodysplastic syndrome (MDS), AF1q copy numbers were 0-6.8 x 10(6)/microg RNA compared with 1.5-2.4 x 10(5)/microg RNA in normal marrow. AF1q levels correlated with international prognostic scoring system (IPSS) scores (P = 0.004) and the risk of post-transplant relapse (P = 0.05). Among IPSS high-risk patients, survival correlated inversely with AF1q levels (P = 0.04). Thus, AF1q levels correlate with high-risk MDS and may provide a marker for risk stratification.