Hypothyroidism and primary hypogonadism are prevalent endocrine disorders with diverse etiologies. Spermatogenesis is regulated by many Y chromosome specific genes. Most of these genes are located in a specific region known as the azoospermia factor (AZF) region in the long arm of the human Y chromosome. Satellited Y chromosome (Yqs) has been regarded as a benign familial variant of no clinical significance; however, considering patient's infertility, if the patient presents with oligospermia/azoospermia, Y chromosome microdeletion analysis for the AZF region should be performed. Patients with these prevalent endocrine disorders are often misdiagnosed resulting in long term treatment. Here we present a case with hypothyroidism and hypogonadism with Sertoli cell only and 46, XY Male with Yq Satellite Chromosome (Yqs).