Analysis of transgenic plants is used today to answer the same questio
ns as ten years ago. Since then, a wide variety of new molecular and b
iochemical technologies, as well as genetic tools, have become availab
le. While there are many technical manuals describing how to use these
tools, much less has been written about when they should and should n
ot, be employed. This gap is important, as poor analysis can easily si
detrack or derail a project. This review addresses appropriate and ina
ppropriate applications of several technologies commonly used for mole
cular and biochemical analysis of transformed plants.