Obstructive sleep apnea (OSA) has long been suggested to increase the risk of development of autoimmune diseases. We investigated the prevalence of Hashimoto's thyroiditis (HT) in 245 euthyroid individuals, who were suspected of having OSA. After polysomnography, subjects were grouped according to apnea-hypopnea index (AHI) consecutively as controls (n=27F/32M, AHI<5), mild-OSA (n=22F/37M, 5≤AHI<15), moderate-OSA (n=23F/38M, 15≤AHI<30) and severe-OSA (n=30F/36M, AHI≥30). Diagnosis of HT based on thyroid ultrasound and positivity of serum anti-thyroglobulin (anti-TG) and anti-thyroid peroxidase (anti-TPO) antibodies. Hashimoto's thyroiditis was diagnosed in 32.2% of controls and in 46.8% of all OSA patients (p=0.03). Severe-OSA patients had the highest HT frequency (51.5%) compared to controls (p=0.02), mild-OSA (42.3%, p=0.03) and moderate-OSA (45.9%, p=0.05) groups. Forty-two of control subjects (71.2%) were negative for both of the anti-TPO and anti-TG, whereas 99 (53.2%) of OSA subjects were positive at least for one of them (p=0.01). HT was detected in 62% of females, 29% of males (p<0.001). Severe female OSA patients had the highest HT prevalence (73.3%), while male control subjects had the lowest (18.7%) among all groups (p<0.001). There was no significant correlation between thyroid volume and severity of OSA but isthmus thickness was significantly correlated to AHI (p<0.01, r=0.22). In conclusion, OSA patients presented higher HT prevalence parallel to severity of OSA, especially among women. These results may lead to further investigations about relation between OSA and auto-immune thyroiditis and to development of screening schemas for severe-OSA patients for early diagnosis of HT before development of hypothyroidism.