Torque teno virus (TTV) is ubiquitous and species-specific, and two different TTV species, Torque teno sus virus 1 (TTSuV1) and Torque teno sus virus 2 (TTSuV2), have been described in domestic pigs and wild boars. Whether these two species are involved in clinical cases of porcine circovirus type 2-associated disease (PCVDs) remains unknown. This study investigates the presence of TTSuV in 85 fetuses, pigs and wild boars infected by PCV2 and affected by PCVDs other than postweaning multisystemic wasting syndrome (PMWS) and porcine dermatitis and nephropathy syndrome. It also explores the genetic diversity of identified strains using phylogenetic analysis. The presence or absence of TTSuV was determined in 85 samples of PCV2-containing organs from 85 infected animals using a specific, one-step PCR method. A nucleotide distance matrix between sequences was computed to infer phylogeny based on a median-joining (MJ) network. TTSuV2 showed high prevalence in animals affected by nephropathy and proliferative and necrotising pneumonia (PNP), and both TTSuV1 and TTSuV2 showed high prevalence in wild boars affected by PMWS. TTSuV1 showed low prevalence in animals affected by nephropathy and PNP, and both TTSuV1 and TTSuV2 showed low prevalence in animals with reproductive disorders. MJ network analysis revealed significant genetic diversity among Croatian isolates.