Donor screening and testing are two mainstays in blood processing centres. Torque teno virus (TTV) is highly prevalent among the general population throughout the world. TTV was discovered in 1997 in the serum of a Japanese patient. TTV is a non-enveloped small virus of 3.8 kb containing a circular single-stranded negative-sense DNA genome. TTV represents the first circovirus-like virus found in humans. The study was conducted to assess the molecular epidemiology of TTV in healthy blood donors and find its relationship with hepatitis B and hepatitis C seropositivity. The study was conducted at the Department of Pathology and Transfusion Medicine, Shaheed Zulfiqar Ali Medical University, Islamabad, from November 2016 to June 2017. Total 282 samples were selected after routine blood screening of Hepatitis B and C, of which 75 were HCV positive (asymptomatic), 75 were HBV positive (asymptomatic) and 132 were from healthy (without HCV and HBV) voluntary blood donors. Selected samples were tested for TTV presence by ELISA and PCR assays. TTV DNA was detected in 55.2% of the healthy donor’s samples. ELISA showed 78/282 positive samples from which 15/75 were HCV positive, 27/75 for HBV and 36/132 TTV positive resulted from healthy donor samples. PCR showed 78/282 positive samples from which 18/75 were positive for HCV, 30/75 for HBV and 30/132 positive for TTV. Collective percentage of TTV prevalence in HCV, HBV and healthy blood donors by ELISA and PCR were 22%, 38%, and 25%, respectively. To conclude, TTV is found with other transfusion transmitted infections, hence, preventive measures should be taken for better health of general population as blood donors represent healthy pool of society. TTV prevalence knowledge in Pakistan will help to develop strategy to control virus transmission in healthy population.