Biological assays, often referred to as woody indexing and herbaceous indexing, may be used to detect and identify plant viruses and other graft-transmissible pathogens to ensure that plants for planting are free from regulated pests. However, many factors can influence the results of biological indexing, which affect the analytical specificity, analytical sensitivity and reliability (repeatability and reproducibility) of these tests. This review focuses on the following: the environmental factors, the role of the inoculum source, the choice of the indicator plant, the expression of symptoms, the number of repetitions, the use of positive controls and healthy controls, the means of transmission of pathogens, the differentiation of strains, the influence of isolates or strains of pathogens, mixed infections, and the bulking of samples for testing. Some indicator plants which are highly susceptible to many viruses and virus-like diseases may be used to detect a wide range of pathogens. However, comparing the results from bioassays with those from serological or molecular tests has shown the limits for detection and identification of many pathogens. It is concluded therefore that biological assays should only be considered for use in conjunction with serological or molecular tests to detect and identify pathogens. Bio-amplification by indicator plants to amplify a pathogen to levels that can be detected by another test method remains of interest.