Introduction: No study has yet been conducted evaluate the factors influencing the growth of patients with congenital hypothyroidism (CH), in Iran. The high prevalence of this disease in Iran, particularly in Isfahan, made it necessary to investigate biomedical diagnostic and early treatment factors potentially affecting growth status among patients with CH.  Materials and Methods: In this prospective cohort study, 760 CH neonates (born 2002-2010), diagnosed and followed up (minimum 1, maximum 5 years) during the CH screening program in Isfahan were enrolled. Height, weight and head circumferences of the patients, during follow up and in subsequent periods, were measured. Diagnostic and therapeutic factors included serum T4 and TSH concentration at diagnosis and after treatment initiation, age at onset of therapy, initial dosage of levothyroxine and age at first normalization of T4 and TSH. Quantile regression for longitudinal data was used for investigating the effects of main factors determining growth development. R free software was used for analyzing data. Results: Longitudinal growth in height and weight was significantly correlated with age at onset of therapy and initial dosage of treatment (p<0.01), while head circumference was associated only with initial dosage (P<0.05). Increase in weight and head circumference were affected by serum TSH concentration at diagnosis (p<0.05), and age of T4 normalization also had significant impact, on some of the proposed quantiles, i.e. weight (p<0.05), height (p<0.01) and head circumference (p<0.001). Conclusion: Among the factors studied, initial dosage of treatment and age at onset of therapy seem to be more important factors for growth development, suggesting that more optimal outcomes are possible through earlier treatment and appropriate levothyroxine dosage.