Oestrogens affect the development and regulation of the immune system. To determine the role of oestrogen receptors α (ER‐α) and β (ER‐β) on the development of the immune system, male ER‐α (ERKO) and ER‐β (BERKO) mice, as well as αβ‐double knockout (DERKO) mice, were studied. Deletion of ER‐α led to hypoplasia of both thymus and spleen. Interestingly, a higher frequency of immature double CD4⁺ CD8⁺ thymocytes was found in ER‐α⁻ mice compared with ER‐α⁺ mice. Female oophorectomized BERKO mice given oestradiol (E2) displayed a similar degree of thymic atrophy compared with the wild‐type strain but showed only limited involution of thymus cortex and no alteration of thymic CD4/CD8 phenotype expression. Our data demonstrate that expression of ER‐α, but not ER‐β, is mandatory in males for development of full‐size thymus and spleen, whereas expression of ER‐β is required for E2‐mediated thymic cortex atrophy and thymocyte phenotype shift in females. A potential background for the above findings may be down‐regulated activity in the growth hormone/insulin‐like growth factor‐1 (GH/IGF‐1) axis in males lacking ER‐α and suppressed sensitivity of females lacking ER‐β to E2‐mediated suppression of IGF‐1.