The vanishing testis with maleness is a rare syndrome with frequency of 1 in 20,000 males. Here, we report about a 30 years old male subject with vanishing testis syndrome, feminization and gynecomastia. Follicle stimulating hormone (FSH) and Leutinizing hormone (LH) levels were elevated whereas testosterone was below normal and anti-mullerian-hormone level was undetectable in the patient. The chromosomal analysis and DNA analysis of SRY and ZFY, DAX-I, AZFa, AZFb, AZFc and heterochromatic region of Y chromosome with STS primer (sY160) were done to detect any genetic changes at specified sites (both at chromosomal and molecular level). Karyotyping confirmed patient as 46, XY male, with no evidence of mosaicism in blood cells. PCR amplification of SRY gene indicated that the SRY gene of the patient was normal. PCR amplification of SRY, ZFY, DAX-I, AZFa, AZFb, AZFc gene and Y chromosome heterochromatic region using STS primer sY(160) did not reveal any microdeletions. The anti-mullerian-hormone level was undetectable indicating that the patient didn't have any testicular tissue in scrotum. Increased levels of FSH, LH and reversed androgen: estrogen ratio might have given rise to gynecomastia in the patient. SRY-positive 46,XY male with vanishing testis might be due to torsion of testis during descent in fetal period. The torsion of testis might have caused vascular occlusion and thereby regression of testicular tissue occurred, but the exact genetic condition yet to understand.