Many viruses have been identified in pericardial fluid and in tissue samples from humans with pericarditis by means of molecular diagnostics. In canine idiopathic pericardial effusion there is as yet no conclusive evidence to support the involvement of an infectious agent. This study was designed to investigate a possible relationship between idiopathic pericardial effusion in dogs and viruses most commonly encountered in humans affected with viral pericarditis. Coxsackievirus B3 RNA, influenza virus type A RNA, human adenovirus type 2 DNA, human cytomegalovirus DNA, and parvovirus B19 DNA were investigated using PCR on pericardial effusion samples and pericardial tissue specimens collected from 14 dogs with idiopathic pericardial effusion. PCR was also used to test for two bacteria, Borrelia burgdorferi and Chlamydia pneumoniae. The same microorganisms were also looked for in pericardial effusions or pericardial washes from 10 dogs with neoplastic pericardial effusion, and in samples collected from 10 dogs which died of a non-cardiac disease. One pericardial effusion sample from a dog with the idiopathic form of the disease tested positive for influenza virus type A and sequencing of the amplicon confirmed the PCR result. In another dog from the same group a cytomegalovirus was detected by PCR in the effusion, but sequencing showed this to be a false-positive result. The genomes of the microorganisms investigated were not detected in neoplastic effusions or pericardial washes. The results indicate that viral and bacterial DNA/RNA of relevance for human pericarditis is rare in pericardial samples from dogs with idiopathic pericardial effusion. The finding of influenza type A viral RNA in pericardial fluid from one dog with the idiopathic form of the disease warrants further investigation.