Hashimoto's thyroiditis is known as thyroid dysfunction and is one of the most common endocrine diseases worldwide. This study seeks to investigate thyroid dysfunction in the male reproductive system. Normal thyroid function is crucial for male reproduction. Semen quality parameters are among the most critical factors affecting male fertility. The main aim of this research was to investigate the effect of thyroid dysfunction on semen quality parameters such as sperm motility, number, and morphology. This cross-sectional retrospective case-control study was conducted between December 2021 and May 2022 in Bahcesehir University Göztepe Medicalpark Hospital Invitro Fertilization center. Patients with Hashimoto's thyroiditis (n=52) were included in the study as the case group. The control group was selected from age and body mass index (BMI)-matched patients who underwent semen analysis (n=57). The participants' age and BMI were 30.90±4.45 and 24.49±1.46, respectively. When we evaluated semen analysis results, we found the number of sperms (p<0.001), motility (p<0.01), and morphology (p<0.001) were significantly better in the controls than in the patients with Hashimoto's thyroiditis. Oligozoospermia, asthenozoospermia, and oligoasthenozoospermia as sperm abnormalities were observed in patients with Hashimoto's thyroiditis. Hashimoto's thyroiditis has a negative effect on semen quality parameters such as sperm motility, number, and morphology. Evaluation of infertile men is recommended in terms of thyroid dysfunction.