The aims of this study were to evaluate torque teno sus virus (TTSuV) infection in healthy slaughter-age pigs and to compare the similarities of the untranslated region (UTR) nucleotide (nt) sequences obtained from different biological samples of the same animals. Fifty-eight pigs were evaluated by PCR assay for the presence of TTSuV in paired samples of liver and serum (Group 1, n = 27) and lung and serum (Group 2, n = 31). All the pigs were positive for TTSuV infection in the organs sampled and 94.8 % (n = 55) presented with viraemia. The nt sequence similarities between the Groups 1 and 2 varied from 91.7 % to 96.6 % (TTSuV1) and 91 % to 95 % (TTSuV2). In Group 1, the nt sequence similarities were 93 % (TTSuV1) and 95.4 % (TTSuV2). In Group 2, the nt sequence similarities were 95 % (TTSuV1) and 91 % (TTSuV2). These results revealed the simultaneous infection with distinct strains of TTSuV1 and 2 in healthy pigs at slaughter age.