Autoimmune disorders may affect reproductive organs including ovaries or lining of the womb (endometrium) in women and testes in men. In women with autoimmune disease effecting ovaries, ovarian reserve (quantity and quality of eggs at any given age) can get prematurely reduced. Therefore, it could shorten the reproductive lifespan of those women. Similarly, the sperm count can prematurely get reduced in men.
Autoimmune conditions, including diabetes, autoimmune thyroid disease, systemic lupus erythematosus etc., are common examples and are associated with reduced fertility. Anti-sperm antibodies can cause infertility in men by reducing the motility of the sperm.