Variety registration is an important area of plant genetic resource characterization and utilization. Within the European Union, varieties must be included on a National List (NL) of a member state or on the Common Catalogue (a compilation of the NLs of the member states) before seed can be sold. This requires a series of tests and trials which assess if the variety is distinct, uniform and stable (DUS) and if it has sufficient value for cultivation and use (VCU). The same DUS criteria are also used world-wide for the granting of Plant Breeders' Rights (PBR), an intellectual property protection system. Both DUS and VCU are currently assessed primarily using field-based trials. However, the potential use of biochemical and molecular markers for DUS purposes is being actively investigated and such markers could have an important role to play in maintaining the quality and scope of PBR in an environment where the increasing number of countries involved in DUS testing and the number of variety comparisons to be made are causing logistical difficulties. More recently, given firstly the increase in the availability of markers from expressed regions of the genome, and secondly the possibilities raised by detailed DNA sequencing programmes and the association of markers (particularly single nucleotide polymorphisms, SNPs) with specific genes, the prospects for a more molecular approach to VCU are also being discussed. This paper reviews the current situation with regard to the use of molecular markers for DUS and VCU testing and considers future prospects for variety registration in the 21st century, ‘-omics’, era.