Regenerated plants derived from somatic embryogenesis, using immature male flower technique of two banana Cavendish cultivars namely 'Grand Naine' and 'Williams', were used for somaclonal variation analysis. Thirty primer combinations of the amplified fragment length polymorphism marker system (AFLP) were used. A total of 1293 and 1302 bands were generated, of which 1275 (98.6%) and 1281 (98.4%) were monomorphic, and 18 (1.4%) and 21 (1.6%) bands were polymorphic in Grand Naine and Williams, respectively. Both cluster analysis of unweighted pair-grouping method with arithmetic averages (UPGMA) and principal coordinate (PCO) analysis separated the two cultivars, and grouped each cultivar with its regenerated plants. AFLP analysis showed 8 and 16 bands specific to the regenerated plants of Grand Naine and Williams, respectively, these were absent in their parents, in addition, we found evidence of the absence of 10 and 5 bands in the regenerated plants, respectively, which were presented exclusively in their parental plants. Such specific bands presented in the regenerated plants could be useful for further investigation on the genetic identification of somaclonal variation in banana. On the other hand, regenerated plants of both cultivars were transferred to the field; no gross phenotypic alteration, e.g. mosaics, variegation, dropping leaves and dwarfs, etc., has been detected until now with the beginning of the flowering period. However, further field evaluation of individual plants is required for the observation of possible phenotypic somaclonal variants that may show useful characters, e.g. resistance to biotic or abiotic stress as well as high yield production and fruit quality.