Porcine circovirus type 2 (PCV2) and hepatitis E virus (HEV) are the most recently recognized causes of infectious hepatitis of pigs and may or may not act independently in the development of the disease. Recently it has been suggested that swine torque teno viruses (TTVs), in co-infections with some swine viral pathogens, may potentiate the severity of disease. In order to search for virological cofactors associated with infectious hepatitis in pigs, we investigated the liver tissues, to determine the presence of TTVs, PCV2 and HEV of naturally infected pigs and analysed the prevalence of both genogroups of the TTVs in the hepatitis lesions. Histopathological techniques, nested-polymerase chain reactions (nPCRs), polymerase chain reaction (PCR) and one-step reverse transcriptase polymerase chain reaction (RT-PCR) were applied to detect hepatitis lesions, TTVs genogroups 1 and 2, PCV2 and HEV infection. Of the livers examined 58% (29/50) had mild to moderate hepatitis and 74% (37/50), 56% (28/50) and 26% (13/50) samples were nPCR, PCR and RT-PCR positive for TTVs PCV2 and HEV respectively. TTVs were detected in 84% (16/19) of the samples which were determined to be of mild severity while present in almost all (90% or 9/10) samples identified as having moderate hepatitis lesions. Additionally, the livers of 12 out of 21 (57%) pigs without the hepatitis lesions were positive for TTVs. These results demonstrate an association between TTVs and infectious hepatitis of pigs in concomitant infections with PCV2 and/or HEV and indicated that TTVs may play a role as a cofactor in the pathogenesis of disease.