Abstract In 2003 an outbreak of sudden deaths occurred in 3–4-week-old piglets on a farm in New South Wales, Australia. There was a marked increase in the birth of stillborn foetuses. Pathological changes consisted of a multifocal non-suppurative myocarditis. A viral infection was suspected but a wide range of known agents were excluded. A modified sequence independent single primer amplification (SISPA) method was used to identify a novel virus associated with this outbreak. Conserved 5′UTR motifs, the presence of a putative N pro coding region and limited antigenic cross-reactivity with other members of the Pestivirus genus, support the placement of this virus in the Pestivirus genus. Phylogenetic analysis of the 5′UTR, N pro and E2 coding regions showed this virus to be the most divergent pestivirus identified to date.