Infertility is estimated to affect about 8-12% of reproductive-aged couples across the globe. It is a clinical manifestation of different etiological factors, which may affect males, females, or both. The distribution of the most common causes affecting female fertility varies among different countries; and in developed countries it usually involves disorders of ovulation, endometriosis, pelvic adhesions, fallopian tube blockage, as well as hyperprolactinemia. Autoimmune diseases may also play a role in female infertility, however, in practice it is often overlooked, as it is not considered to be a major cause of female infertility. Nevertheless, we have to be aware of the possible contribution to the diagnosis of infertility, as well as the effect of the treatment of infertility on the course of the disease. As there is an overall increased prevalence of women with autoimmune disorders seeking infertility treatments, the objectives of this paper were to: a) assess the association between potential fertility impairment and several autoimmune diseases; including systemic lupus erythematosus, antiphospholipid syndrome, autoimmune thyroid disease, rheumatoid arthritis, inflammatory bowel disease, and Behçet’s disease; b) learn whether assisted reproductive techniques and the associated hormonal stimulation, may confer additional risk in patients with autoimmune diseases, such as disease flares and other maternal complications; c) learn whether assisted reproductive techniques outcome may be potentially impaired by the underlying disease. A literature search on PubMed showed 109 related articles. There were 63 relevant articles that were included in this review. When considering all included articles, assisted reproduction generally seems to be safe in patients with the autoimmune diseases mentioned above; however, it is of great importance that the patients are in stable disease remission, and adequately treated. Nevertheless, the available data concerning the relationship between complications associated with the above mentioned diseases and assisted reproduction, seem to be very limited and somewhat controversial, and further research is therefore needed to better understand these issues.