Congenital hypothyroidism (CH) is defined as congenital thyroid hormone deficiency. The aim of this study was to examine the DNA and neuron damage in rat pups with CH and to evaluate the beneficial effects of 3.6-Dibromo-alpha-[(phenylamino) methyl]-9H-carbazole-9-ethanol (P7C3). Rat pups were assigned to four groups as Group 1: CH, Group 2: CH treated with P7C3, Group 3: CH treated with P7C3 and L-thyroxine, and Group 4: control group. Plasma 8-(OH) DG and neuron-specific enolase (NSE) concentrations were determined in all groups. For histopathological examinations haematoxylin-eosin staining was applied. Increased NSE concentrations were found in the CH group compared to the control group. The 8-(OH) DG concentrations were found to be higher in Group 2 and Group 3 than in the control group. Neuronal degenerations localized in the hippocampus and brain cortex were found in histopathological examinations in Group 1. The distribution of neuronal degeneration was less in Group 2 and Group 3 than Group 1 and lesser in Group 3 than in Group 2. DNA damage might have a role in CH pathogenesis. P7C3 compounds have a protective effect in CH.