A mutation in the thyroglobulin (Tg) gene is the primary cause of hereditary dwarfism and hypothyroidism in the rdw rat. Despite the Tg mutation that causes a Tg shortage, rdw rats survive. The present study examines the influences of this condition on the pancreatic proteome. Normal control (group 1; n = 19) and rdw rats that did not receive L-thyroxine (T4) (group 2; n = 27) were sacrificed from 4 to 56 weeks after birth. The rdw rats were supplemented either with daily intraperitoneal injections of T4 from 3 to 28 days after birth (group 3; n = 4) or with normal thyroid tissues grafted at 4 weeks of age (group 4; n = 3). Groups 3 and 4 were sacrificed 12 weeks after birth. Pancreatic proteomes analyzed by two-dimensional gel electrophoresis showed that levels of at least four pancreatic proteins were higher in group 2 than in group 1, and that those of four were lower. Cluster decomposition and principal component analysis of the eight protein contents showed that groups 1 and 2 were separated into two clusters and that pancreatic proteomes of group 4 were better normalized than those of group 3. Injecting T4 into group 3 was temporarily effective, whereas the thyroid graft to group 4 provided a continuous positive effect, which concurred with the increased body weight of the other two groups of rdw rats that received grafts of normal thyroids.