Dyslexia and dyscalculia originate from the joint effects of multiple genetic and environmental factors on the developing brain in the first years of life, including the prenatal phase. While many candidate genes have been reported in the literature (e.g. DCDC2, DYX1C1, KIAA0319, and ROBO1), so far no DNA variants have revealed reliable associations across the whole genome. Moreover, potential early environmental influences (e.g. preterm birth, prenatal substance exposure, breastfeeding, maternal psychosocial stress, developmental toxicants) currently preclude specific interpretations since they also have a genetic basis that is typically not controlled in existing studies. Correspondingly, the question of how gene–environment correlation and interaction lead to learning difficulties can only be answered at a very general level at present.