The burden of endocrine disorders, especially thyroid and women reproductive gland dysfunction and its related disease numbers are rapidly increasing for the recent years. Determining prevalence of thyroid disease among population with serum TSH level, primary hypothyroidism is more common than secondary hypothyroidism (1000:1) for all age and gender. In the statistical report of Center for Health Development in 2013, there were 2615 female patients with thyrotoxicosis (E05) registered which more than 531 female patients with hypothyroidism (E00-E02). Therefore, we studied bone mineral density changes due to thyroid dysfunction in female patients. Ovarian dysfunction and irregular menstrual period during hypothyroidism can cause of sexual dysfunction and infertility. Early screening, right diagnosis and treatment for hypothyroidism can prevent from infertility caused by thyroid dysfunction.We used a hospital-based case-control study design. In the study 90 reproductive age (15-49) female patients were participated. 60 of them were evaluated as relatively healthy patients and 30 of them were diagnosed by laboratory test with hypothyroidism. Serum level of TSH, fT3, fT4, estradiol and progesterone (TSH, fT3, fT4, E2, P4 TOSOH Corporation, Tokyo, Japan) were evaluated by ELISA. The ovarian function was evaluated by ultrasound (Hitachi alokа-Prosound alpa F37, Japan) and ovarian follicle numbers were counted at the 3-5th and 10-15th day of menstruation cycle.Total 90 patients ranging 24-46 years old (average age was 33.4±5.7 in control group, 35.5±6.1 in hypothyroid group) were participated. Comparison of fT3 and fT4 average level between control (fT3 2.47±0.34 pg/ml, fT4 1.23±0.19 ng/dL) and hypothyroid group (fT3 2.48±0.31 pg/ml, fT4 1.07±0.14 ng/dL), fT3 wasn’t statistically relevant (p>0.05) but, fT4 was statistically relevant (p<0.05). The average level of TSH in incidental group (4.24±1.55 µIU/ml) was 2.4 times higher than control group (1.79±0.4 µIU/ml) seems subclinical hypothyroidism. Comparison of estradiol and progesterone average level between hypothyroid group (estradiol 41.6±9.9 pg/ml and progesterone 0.32±0.3 pg/ml) and control (estradiol 41.3±9.0 pg/ml and progesterone 0.38±0.2 pg/ml) at the 3rd day of menstrual cycle, in the ovarian follicle phase, there weren’t statistically relevant (p>0.05). Comparison of estradiol and progesterone average level between hypothyroid group (estradiol 185.4±54.7pg/ml and progesterone 0.8±0.6 pg/ml) and control (estradiol 224.6±76.8 pg/ml and progesterone 0.8±0.5 pg/ml) at the 10th day of menstrual cycle, in the ovarian follicle phase, were statistically relevant (p<0.01). For the progesterone hormone, there was no statistical relevance (p>0.05). The ovarian dominant follicle size was 16.2±2.5 mm in the hypothyroid group and 17.6±2.1 mm in the control group. The dominant follicle size have statistical relevance as 2 groups (p<0.01). Comparison of estradiol and progesterone average level between control (estradiol 139.8±42.9 pg/ml and progesterone 15.0±4.1 pg/ml) and hypothyroid group (estradiol 158.9±75.2 pg/ml and progesterone 12.1±5.3 pg/ml) in the lutein body phase, serum progesterone level was decreased during hypothyroidism (p<0.01). The increased serum level of fT4 can expand serum fT3 as well (r=0.218, p=0.039). The increased serum TSH was inversed correlation to fT4 (p<0.01, r= -0.420). The increased serum TSH was inversed correlation to progesterone (P<0.05, r= -0.234). Ovarian follicle size are direct correlation to increased serum estradiol (r=0.507, p<0.01).The serum TSH level were extremely increased during hypothyroidism (p<0.001). Serum female hormone level was decreased depending on the fT3, fT4 and TSH level for patients with hypothyroidism.