In this study, the etiological factors, diagnostic approaches, dose, and duration of treatment were compared between cases with transient and permanent congenital hypothyroidism (CH) with respect to prognosis. One hundred and twenty-two patients who received treatments with the diagnosis of CH in the last 10 years were included in the study. The records of the patients were reviewed retrospectively. Serum thyroid-stimulating hormone (TSH) levels at the time of diagnosis were found to be significantly higher, and total thyroxine (TT4) levels were found to be significantly lower in the permanent CH group in comparison to the transient CH group. A statistically significant difference was present between the groups regarding treatment doses, the time needed for TSH decrease to <5 mIU/ml and the TSH and free thyroxine (FT4) levels obtained one month after discontinuation of the treatment. The association between age at the time of initiation of treatment and results of Denver Developmental Test was noted to be statistically significant. The high frequency of transient CH in our region leads to the result that some of the patients had to be unnecessarily treated with L-thyroxine for a long time.