As academic achievement can have a major impact on the development of social inequalities we set out to explore how performance differences arise. Using data of the German twin study TwinLife, genetic and environmental effects on school grades in mathematics, German and the grade point average in two age cohorts (11 and 17 years old) were identified. Structural equation modelling on the data of 432 monozygotic and 529 dizygotic twin pairs as well as 317 siblings of the twins showed substantial genetic effects (up to 62%) in both cohorts on all three variables. Next to genetic influences, the twin-specific environment as well as non-shared environmental influences were found to explain the interindividual differences in mathematics and German as well as the grade point average. A cohort effect showing itself in higher heritability in the older cohort was found for mathematics and the grade point average but not for German. Moreover, we compared twins who were assigned to the same classroom to those twins who were assigned to different classrooms and found lower effects of the twin-specific shared environment in the latter group. Our study thereby contributes to the understanding of the etiology of interindividual differences in academic achievement in the numeracy and literacy domain in two age cohorts.