Differences exist among inbred mouse strains in the size of the thymus relative to overall body size. These differences are controlled by several genes acting in different phases of thymus development. After 50 days of age, there is an approximately 2-fold difference in thymus size between C57BL/6J and AKR/J, and other strains (A/J, DBA/2J, BALB/cJ, CBA/J, C3H/HeJ, 129/J, C57BL/10J, MA/MyJ). The C57BL/6J and AKR/J mice have the larger thymus, and this characteristic is dominant in F1 animals derived from C57BL/2J and A/J strains. Studies on recombinant inbred strains derived from C57BL/6J and DBA/2J (BXD strains), and C57BL/6J and A/J (AXB and BXA strains) indicate that this difference is controlled by alleles at one locus, which we have designated Tsz-1 (thymus size 1). In the immediate postnatal period (0–23 days), while the relative size of the thymus is increasing, the thymus size of C57BL/6J mice is large relative to that of A/J mice, but the A/J character is dominant during this period, and this difference appears to be controlled by two genes.