The Eurasian Scops Owl Otus scops is a migratory owl whose population is declining throughout a large part of its breeding range, due to intensification of farming practices and land-use changes. For this reason, it is considered the most threatened owl in Europe. Several raptor species like Scops Owl present limited possibility to differentiate between sexes, due to the reduced biometric and morphometric differences. The availability of a reliable method to sex Scops Owl through biometric measurements would facilitate the study of sex-related survival, movements and behavior characteristics of this species, improving conservation management projects. In the current study, we developed a cost-effective and accurate method of sexing Scops Owl, based on discriminant analysis of morphometry. One hundred and five birds were captured, sexed using genetic methods and biometric measures were taken. A GLM model was built to evaluate the biometric measures statistically linked to the sex. The best model (AIC = 49.211) selected three biometric measures: wing length, tail length, weight. The results of the model were used to derive models scores, and the predictive probability of male and female to be correctly identified was estimated. The discriminant function provides an accurate method of sexing Scops Owl in the hand.