Background: Congenital hypothyroidism (CH) is a common endocrine disease and an important cause of mental retardation. The purpose of this study was to investigate the probable role of season and climatic factors in the incidence of CH in Kerman province, Iran. Methods: Incidence data were collected from the CH screening program files from 2005 to 2011 in Kerman province, a number of 288,437 infants were included in the study. Climate data were collected from the Meteorological Office. The relations were tested by chi(2)-test, Pearson correlation, and negative binomial regression. Results: The overall incidence of CH in Kerman province was 2.68 per 1000 births. There was a significant difference in both the monthly and seasonal incidence of CH (p < 0.05). There were a few significant, but weak correlation between some climatic factors and the incidence of CH in some regions, but the results were inconsistent. Conclusions: It seems like there is no clear relation between CH incidence and climate factors, in Kerman Province. However, CH incidence was highest in October (Autumn) and lowest in June (Summer).