The main goal of this review is to provide some guidelines for choosing a p
roper method when searching for differentially expressed transcripts. The c
hoice of an approach should depend upon particular features of the experime
nt and project requirements. We outline some general considerations to help
decide between differential display-related techniques and subtractive hyb
ridization. While discussing advantages and problems of differential displa
y, special attention is given to several recently developed methods based o
n alternative principles of fingerprint production, which provide a possibi
lity for complete systematic investigation of RNA samples.