Callosal connections were studied with tracers (horseradish peroxidase (HRP) and wheat germ agglutinin‐horseradish peroxidase (WGA‐HRP)) in normal rats and rats deprived of thyroid hormones with methimazole (Sigma) since embryonic day 14 and thyroidectomized at postnatal day 6. In hypothyroid rats, the auditory areas, in particular the primary auditory area, showed cytoarchitectonic changes including blurred lamination and decrease in the size of layer V pyramidal neurons. In control rats, callosally‐projecting neurons were found between layers II and VI with a peak in layer III and upper layer IV. In hypothyroid rats, labelled neurons were found between layers IV and VI with two peaks corresponding to layer IV and upper layer V, and in upper layer VI. Quantitative analysis of radial distribution of callosally‐projecting neurons confirmed their shift to infragranular layers in hypothyroid rats. Three‐dimensional reconstructions showed a more continuous tangential distribution of callosally‐projecting neurons in hypothyroid rats which may be due to the maintenance of a juvenile ‘exuberant’ pattern of projections. These changes in cortical connectivity may be relevant for understanding epilepsy and mental retardation associated with early hypothyroidism in humans and to clarify basic mechanisms of cortical development.