Identification of the sex of birds is important for captive breeding of endangered species. In the oriental white stork (Ciconia boyciana), an endangered species, both sexes produce an acoustic signal called “clatter” by rattling their mandibles together to generate sounds. We examined the structure of male and female clatter to determine whether clatter is sexually dimorphic. The acoustic structure of the clatter of the two sexes proved to be dimorphic with respect to the fundamental frequency; female clatter had higher fundamental frequencies. The fundamental frequency correlated significantly and positively with bill length, suggesting that bill morphology contributes to the sexual dimorphism of clatter. Sexing can be done by acoustic signals without capturing birds, and thus is useful as a non-invasive sexing method for ecological and conservation studies of birds.