Plant transformation has become an important experimental tool for investigations into various aspects of plant biology such as physiology, genetics, developmental biology, molecular biology etc. The precision and simplicity of the approach coupled with the power of resolution of details at the molecular level have led to its adoption to answer hitherto intractable problems. In addition, the feasibility of mobilizing and expressing foreign genes into plants has opened up whole new era of genetically engineered crop plants capable of defending against biotic and abiotic stresses and producing better quality products or novel compounds of pharmaceutical and industrial value. There are, however, aspects of plant transformation that are not well understood and cause considerable variation among independent transgenics produced under identical conditions. In this article eve discuss various factors that contribute to variation among transgenics and suggest experimental approaches for genetic and molecular analyses of transgenics to derive meaningful conclusions. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.