The present study was designed to investigate the prevalence of swine Torque teno virus (TTV) in post-weaning multisystemic wasting syndrome (PMWS)-affected and non-affected Spanish swine. Nested PCR (nPCR) assays to detect two distinct TTV genogroups were applied. A significantly higher prevalence of TTV infection was found in sera from PMWS-affected animals (97 %) than in sera from non-PMWS-affected animals (78 %). Whilst PMWS-affected pigs (91 %) were more likely to be infected with TTV from genogroup 2 than non-PMWS-affected swine (72 %), no such difference was observed with genogroup 1. Nucleotide sequences of nPCR products were 91-99 % identical between strains within a genogroup. In contrast, inter-genogroup sequence identities were 49-58 %. Phylogenetic analyses demonstrated that genogroups form different clusters without association with PMWS or porcine circovirus type 2 infection status of the animals. These results indicate a high prevalence of both swine TTV genogroups in Spain, being present more frequently in PMWS-affected animals than in non-PMWS-affected animals. © 2006 SGM.