Developmental iodine deficiency leads to inadequate thyroid hormone, which damages the hippocampus. In the present study, we implicate hippocampal caveolin‐1 and synaptophysin in developmental iodine deficiency and hypothyroidism. Two developmental rat models were established: pregnant rats were administered either an iodine‐deficient diet or propylthiouracil (PTU)‐adulterated (5 p.p.m. or 15 p.p.m.) drinking water from gestational day 6 until postnatal day (PN) 28. Nissl staining and the levels of caveolin‐1 and synaptophysin in several hippocampal subregions were assessed on PN14, PN21, PN28 and PN42. The results obtained show that surviving cells in the iodine‐deficient and PTU‐treated rats were lower than in controls. Up‐regulation of caveolin‐1 and down‐regulation of synaptophysin were observed in the iodine‐deficient and PTU‐treated rats. Our findings implicate decreases in the number of surviving cells and alterations in the levels of caveolin‐1 and synaptophysin in the impairments in neural development induced by developmental iodine deficiency and hypothyroidism.