Previous studies have shown that homosexual men differ from heterosexual men in several somatic traits and lay people accurately attribute sexual orientation based on facial images. Thus, we may predict that morphological differences between faces of homosexual and heterosexual individuals can cue to sexual orientation. The main aim of this study was to test for possible differences in facial shape between heterosexual and homosexual men. Further, we tested whether self-reported sexual orientation correlated with sexual orientation and masculinity-femininity attributed from facial images by independent raters. In Study 1, we used geometric morphometrics to test for differences in facial shape between homosexual and heterosexual men. The analysis revealed significant shape differences in faces of heterosexual and homosexual men. Homosexual men showed relatively wider and shorter faces, smaller and shorter noses, and rather massive and more rounded jaws, resulting in a mosaic of both feminine and masculine features. In Study 2, we tested the accuracy of sexual orientation judgment from standardized facial photos which were assessed by 80 independent raters. Binary logistic regression showed no effect of attributed sexual orientation on self-reported sexual orientation. However, homosexual men were rated as more masculine than heterosexual men, which may explain the misjudgment of sexual orientation. Thus, our results showed that differences in facial morphology of homosexual and heterosexual men do not simply mirror variation in femininity, and the stereotypic association of feminine looking men as homosexual may confound judgments of sexual orientation.