The lack of naturally occurring resistance to white clover mosaic virus (WCMV) has demanded exploration of a transgenic approach for the development of WCMV-resistant white clover plants. Transgenic white clover plants producing sense (co-suppression), antisense and hairpin RNA (hpRNA) transcripts corresponding to the WCMV replicase gene were produced and analysed at the molecular and phenotypic levels. Expression of hpRNA and antisense transgenes provided a high level resistance to WCMV, while the sense transgene provided partial resistance. The presence of small interfering RNA molecules (siRNAs) in the transgenic white clover plants prior to virus challenge indicated that WCMV resistance was due to pre-activated RNA silencing, and the presence of siRNAs acted as reliable biomarkers for prediction of the degree of virus resistance in these plants.