Recently, different methodological approaches have been discussed as an explanation for inconsistencies in studies investigating sex differences in different intelligences. The present study investigates sex differences in manifest sum scores, factor score estimates, and latent verbal, numerical, figural intelligence, as well as fluid and crystallized intelligence as measured by the German Intelligence-Structure-Test 2000-R (IST 2000-R; Liepmann, Beauducel, Brocke, & Amthauer, 2007). The not population-representative sample consisted of 977 German 11th and 12th graders enrolled in a "Gymnasium" (551 female; mean age: M = 16.70; SD = 0.65) who completed the IST 2000-R. Sex differences in fluid and crystallized intelligence were not influenced by the method applied with men performing better than women. However, extent and direction of sex differences in verbal, numerical, and figural intelligence differed by the method applied. Whereas there was a male advantage in all three factors measured as manifest sum scores, women performed better in verbal intelligence as measured by factor scores or as latent variables. Effect sizes of sex differences in numerical and figural intelligence were also greatly reduced when applying the latter two methods. Results are discussed with regard to their theoretical and practical implications. (Contains 2 figures and 3 tables.)