For efficient in vitro multiplication of plants, every step of micropropagation should be taken care at in order to prevent contamination. Indexation of stock plants, explants and cultures for contaminants is based on a series of morphological, physiological and biochemical tests, which can be supplemented with modern methods. To ensure that the material is free from the major pathogens, rapid, sensitive and specific diagnostic methods are required. The identification methods used for diagnosis and detection of plant tissue contaminants are based on two main strategies: 1) for identification of new species of contaminants it is recommended to use: - serological tests, nutritional kits, tests incorporating chemotaxonomic markers (based on proteins and fatty acids) - a comparison of phenotypic or genetic profiles including those based on restriction or amplification of fragment length polymorphism of DNA 2) for classification of new species it is recommended to use: - reagents (as antisera, nucleic acids probes, oligonucleotide primers) for polymerase chain reaction (PCR) - general methods of comparison of the test strain with a reference strain. Antibiotics or fungistatics should be applied in tissue culture to eliminate identified contaminants. Treatment of index-negative explants with combinations of antibiotics is the most effective method to eliminate contaminents from plant tissue culture. Because of high costs of treatment and their phytotoxicity, antibiotics should only be used against identified contaminants from valuable mother plants.