Introduction: There is no definitive finding about the association between vitamin D deficiency and autoimmune hypothyroidism. On the other hand, there is evidence that trace elements such as zinc undergo changes in the presence of hypothyroidism. This study was aimed to compare the prevalence of vitamin D and zinc deficiency in patients with hypothyroidism and healthy people in Birjand in the winter of 2016. Materials and Methods: In this case control study, 50 hypothyroid patients referred to endocrinology clinic of Vali-e-Asr Hospital in Birjand and 50 healthy subjects were selected from the general population. The two groups were matched in terms of age, gender and body mass index. After obtaining informed consent, blood samples received from participants and sent to laboratory for Vitamin D, Ca, Zinc, TSH and Anti TPO measurement. Data were analyzed by SPSS version 19 with the help of Chi-square, independent T test, Mann Whitney test, Pearson and Spearman Correlation tests and logistic regression test. P<0. 05 was considered statistically significant. Results: Overall 88% of patients and 68% of healthy subjects suffered from vitamin D deficiency (P = 0. 016). 16% of the case group and 4% of the control group suffered from zinc deficiency (P = 0. 046). In the case group, TSH was inversely and significantly associated with vitamin D (r =-0. 530, P <0. 001) and calcium (r =-0. 551, P <0. 001) and correlated directly and significantly with Anti TPO (r = 0/628, P <0. 001). Also Anti TPO was inversely and significantly correlated with vitamin D (r =-0. 286, P = 0. 44). Conclusion: The results of this study showed that the prevalence of vitamin D and zinc deficiency in patients with hypothyroidism is significantly higher than the normal people. It is recommended that people with hypothyroidism be monitored for vitamin D and zinc deficiency.