A high level of genetic purity in crop varieties must be achieved and maintained for agronomic performance as well as to encourage investment and innovation in plant breeding and to ensure that the improvements in productivity and quality imparted by breeders are delivered to the farmer and, ultimately, to the consumer. Traditionally, morphological comparisons have formed the basis for genetic purity evaluations. However, replicated field observations are time-consuming, expensive and unreliable. Morphology cannot provide information on the purity of specific genetic attributes that relate to grain quality or to pest or herbicide resistance bred into varieties. Biochemical assays, including isozymes, can distinguish varieties within several species. Isozymes have been routinely used in checking seed-lot purity in maize (Zea mays L.) for the past 20 years. Newer DNA-based technologies such as restriction fragment length polymorphisms and more recently developed methods that use the polymerase chain reaction can allow even more discriminative and faster identification of varieties. However, none of the DNA methods have replaced biochemical methods for seed purity assays, other than in a relatively select group of crops with very high seed value, due to their high datapoint cost. It will require further miniaturization, automation and enhanced capabilities to process numerous samples simultaneously before newly developed methods supplant biochemical methods for routine usage in purity testing. New varieties that have major genes for herbicide or insect resistance incorporated within them require purity assays during product development and following seed production of the commercial variety. Immunological or DNA sequence assays can be developed and automated systems are required to process hundreds of thousands of individuals. Ultra-high, micro-array technologies and single-molecule detection systems are now under development. These technologies offer the promise that adequate distinction and high sample throughput will be combined. New methods may eclipse the capabilities of biochemical methodologies, thereby potentially raising genetic purity standards and enabling farmers and consumers better to utilize and benefit from increasingly productive varieties that are bred from a more diverse base of genetic resources.