The secretor status of ABH antigens, determined by FUT2 polymorphisms, affects susceptibility to various infectious diseases. In addition to many SNPs responsible for the nonsecretor phenotype, five nonfunctional alleles (se) resulting from copy number variations have been reported. One of the five alleles generated by an unequal crossover between FUT2 and a pseudogene (SEC1), is se(fus). This allele may be misidentified as a functional allele if only common inactivating SNPs are genotyped because it contains the 3MODIFIER LETTER PRIME region of the functional FUT2. Therefore, accurate detection of se(fus) is desirable. For this purpose, a high-resolution melting (HRM) analysis is developed for detection of se(fus) in which a 284bp fragment of SEC1 and se(fus) but not FUT2, are amplified. This HRM analysis detected se(fus) reliably. Thus, an initial screening or prescreening for se(fus) using HRM analysis seems to be useful for association studies of FUT2.