In banana tissue cultures, the occurrence of dwarf off types is a common phenomenon and their detection become relevant. In this study, tissue culture derived (somaclonal) and radiation-induced off types in banana cultivars. Robusta and Giant Cavendish were analyzed using a SCAR-based molecular diagnostic technique. The dwarfs were initially characterized at maturity, by height, leaf shape, pseudostem height and other agronomic characters. At the molecular level, amplification with the SCAR primer resulted in an expected amplified fragment of 1500 bp in normal but not in the dwarf types. Further in a multiplex PCR, an internal positive control was included using primers for 18S rRNA which gave amplification in both the normal and dwarf types. This study shows that the dwarf off-types isolated through tissue culture and radiation-mutagenesis were true dwarfs, validated by using the dwarf-specific RAPD marker for banana.