The human secretor α(1,2) fucosyltransferase encoded by the FUT2 determines the production of ABO(H) antigens in secretions. Recent studies demonstrated the presence of several nonfunctional alleles in the FUT2. During the analysis for inactivating mutations at the FUT2 locus from 24 Samoan and 47 Bangladeshi individuals, we found two distinct Alu‐mediated deletions of FUT2. The FUT2 deletion in a Bangladeshi population was identical with that found in Indian individuals with the Bombay phenotype (sedel), but not associated with the null allele (T725G) of the H gene (FUT1). The FUT2 deletion in Samoans is a novel null allele (sedel2). The junction region of sedel2 was successfully amplified using the same primers for the sedel amplification. DNA sequencing of the junction region of the sedel2 indicated that there was a 32‐bp sequence identity between DNA sequences surrounding the 5′ and 3′ breakpoints. The size of the deletion of the sedel2 was 9.3 kb, including the full coding region of FUT2. The frequency of the sedel in a Bangladeshi population was 0.074, and that of the sedel2 in a Samoan population was 0.104. Hum Mutat 16:274, 2000. © 2000 Wiley‐Liss, Inc.