Background: Fanconi anemia (FA) is a rare, autosomal recessive (AR) and multifactorial disorder. A high prevalence of FA observed in Iran is perhaps due to the high rate of consanguineous marriages. This study investigates the extent of short stature in patients with FA, the frequency of hypothyroidism in FA and the correlation between height and hypothyroidism. Methods: Eighteen patients with FA referred to the Pediatrics Clinic of Nemazee Hospital were selected based on specific congenital and malformational symptoms and bone marrow results. These patients were evaluated for weight, height, bone age, clinical goiter and thyroid function tests. Results:Eleven out of 18 patients (61%) had overt or compensated hypothyroidism. Short stature was found in 89% of patients with a mean height more than two standard deviation (SD) below the mean height for that age. There was no significant correlation between short stature and overt or compensated hypothyroidism. The mean height standard deviation score (SDS) of patients with normal thyroid function was also more than two SD deviation below the normal mean, revealing that short stature is an inherent feature of FA. In seven cases with goiter, only three had hypothyroidism. The mean±SD weight SDS was -1.03±0.99. The mean±SD bone age was 12±4.5 yr. Conclusion: According to the results of this study, our patients had a considerable prevalence of hypothyroidism and short stature was a common feature of FA. It is recommended that thyroid function test is necessary in these patients.