It is well known that female infertility is multifactorial. Therefore, we aimed to compare the effects of thyroid dysfunction, vitamin deficiency, and microelement deficiency in fertile and infertile patients. Between May 1st, 2017, and April 1st, 2019, we conducted a retrospective case-control study with of 380 infertile and 346 pregnant patients (who normally fertile and able to conceive spontaneously). The fertile patients were selected among those who got pregnant spontaneously without treatment, had a term birth, and did not have systemic or obstetric diseases. The levels of thyroid-stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), anti-thyroid peroxidase (anti-TPO), vitamin D, vitamin B12, folic acid, ferritin, and zinc of both groups were compared. There was no difference between patients in the infertile and pregnant groups in terms of low normal and high serum T3 and T4 levels (p = 0.938; p > 0.05) respectively, nor in terms of normal and high anti-TPO levels (p = 0.182; p > 0.05) respectively. There was no significant difference regarding patients with low, insufficient, and sufficient vitamin D levels in the infertile and pregnant groups (p = 0.160; p >0.05) respectively. The levels of folic acid, ferritin, and zinc of the infertile group were significantly lower than those of the pregnant group. The serum levels of folic acid, ferritin, and zinc in infertile patients presenting to our outpatient clinic were lower than those o the fertile patients.