Introduction: There is a lack of national/regional data on the relationship between breast cancer and thyroid diseases and the limited data available are controversial. This study was designed and conducted to investigate thyroid autoimmunity in women with newly diagnosed breast cancer. Methods and Materials: In a case-control study, 40 women with confirmed diagnoses of breast cancer and 40 age-matched healthy counterparts were recruited during a 12-month period from outpatient clinics of the Tabriz University of Medical Sciences. The case group were enrolled for the study before receiving treatment. Thyroid and physical examination was carried out in all participants and serum levels of TSH, FT4, ATPO and ATG were determined. The results were compared between two groups, and different histopathological subgroups of breast cancer. Results: The mean age was 49.48±7.75 and 46.80±7.00 years in the case and control groups respectively. Thyroid and physical examination were normal in all participants. TSH, ATPO and ATG serum levels were comparable between the two groups however, the median level of serum FT4 was significantly higher in the case group (1.20 μg/dl vs. 1.03 μg/dl p<0.001). Increased levels of serum TSH and FT4 were found in 7.5% of the cases, while there were decreased levels in 2.5% of the cases, with no significant differences between the two groups. Thyroid tests were comparable between the different histopathological subtypes of breast cancer. Conclusion: No relationship was found between thyroid autoimmunity and breast cancer, a finding in concordance with some reports and in contrast with others. It seems that further studies with larger sample sizes are needed for conclusive findings.