The aim: The objective of the study is to investigate whether in vitro fertilization (IVF) procedures in patients with autoimmune thyroid disorders increase the likelihood of conception and delivery. Patients and methods: The study included 275 patients who had been treated for infertility at the Clinical Hospital Center Rijeka between 2009 and 2017, either conservatively or with IVF. In all the participants thyroid function was assessed by measuring serum concentrations of thyroid-stimulating hormone (TSH), free thyroxine (FT4) and free triiodothyronine (FT3), while thyroid autoimmunity was assessed by measuring thyroid peroxidase antibodies (TPOAt) and thyroglobulin antibodies (TgAt) in the serum samples, as well as by thyroid ultrasound examinations. The reproductive outcomes were compared between the infertile patients and the patients with normal hormone levels, negative thyroid antibody tests and normal ultrasound findings. The flow cytometry analysis was used to investigate the blood and follicular fluid mononuclear cells in patients treated with IVF. Results: In the group of patients with autoimmune thyroid disorders treated with IVF, significantly less women conceived and significantly more women experienced spontaneous abortions compared to the women with normal thyroid tests. The ratio of the number of births to the number of conceptions did not significantly differ between the two groups. There was a significantly lower proportion of natural killer cells in the follicular fluid of the patients with positive thyroid autoantibodies compared to patients with no thyroid autoantibodies. Conclusion: IVF procedures significantly increase probability of conception in patients with subclinical autoimmune thyroid disorder, but not probability of delivery. Despite euthyroid status as a result of levothyroxine replacement, the risk of spontaneous abortions was increased in patients with autoimmune thyroid disorders, regardless of the type of infertility treatment (conservative or IVF).