The breast cancer resistance protein, also known as ABCG2, is one of the most studied ATP-binding cassette (ABC) transporters, due to its ability to confer multidrug resistance1,2. The lack of information on the physiological roles of ABCG2 in humans severely limits cancer chemotherapeutic approaches targeting this transporter. We report here that ABCG2 comprises the molecular basis of a new blood group system (Junior, Jr), and that individuals of the Jr(a−) blood type have inherited two null alleles of ABCG2. We thus identified 5 frameshift and 3 nonsense mutations in ABCG2. Furthermore, we show that the prevalence of the Jr(a−) blood type in the Japanese and European Gypsy populations is related to the mutations p.Q126X and p.R236X, respectively. The identification of ABCG2−/− (Jr(a−)) individuals, who appear phenotypically normal, is an essential step towards targeting ABCG2 in cancer, but also understanding the physiological and pharmacological roles of this promiscuous transporter in humans.