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The commercial multiplication of a large number of diverse plant species represents one of the major success stories of urilizing tissue culture technology profitably. Micropropagation has now become a multibillion dollar industry, practised all over the world. Of the various methods used to micropropagate plants, somatic embryogenesis and enhanced axillary branching have become the principal methods of multiplication. Long-term benefits of this enterprise, however, lie in the production of clonally uniform plants. The concept of genetic uniformity among micropropagated plants derived through organized meristems was exploded by several convincing reports of the incidence of somaclonal variation at morphological, cytological (chromosome number and structure), cytochemical (genome size), biochemical (proteins and isozymes), and molecular (nuclear and organellar genomes) levels. Somaclonal variation is not limited to any particular group of plants; it has been reported, for example, in ornamentals, plantation crops, vegetable and food crops, forest species and fruit trees. The upsurge of these reports, facilitated to a large extent by the technical developments made in molecular biology, is a matter of great concern for any micropropagation system. The economic consequences of somaclonal variation can be enormous in forest trees and woody plants, as they have long life cycles. Therefore, somaclonal variation has to be dispensed with if large-scale micropropagation of diverse plant species is to become not only successful but also accepted by end-users. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that lead to somaclonal variation of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach, especially at the DNA sequence level, initially and at various cultural stages, is essential. The results obtained at early multiplication stages from these tests could help in modifying the protocol/s for obtaining genetically true-to-type plants, and ultimate usage by entrepneneurs without any ambiguity.