Management of patients diagnosed with localized prostate cancer is complica
ted by the diverse natural history of the disease and variable response to
treatment. Prognostic criteria currently in use cannot fully predict tumor
behavior and thus limit the ability to recommend treatment regimens with th
e assurance that they are the best course of action for each individual pat
ient. The search for better prognostic markers is now focussed on the molec
ular mechanisms which underlay tumor behavior, such as altered cell cycle p
rogression, apoptosis, neuroendocrine differentiation, and angiogenesis. As
the number of potential molecular markers increases, it is becoming eviden
t that no single marker will provide the prognostic information necessary t
o make a significant improvement in patient care. In addition, it seems lik
ely that traditional methods of assessing the prognostic value of this mult
itude of new markers will prove inadequate. In this review, we briefly exam
ine the current state of prognostication in localized prostate cancer and s
ome of the promising new molecular markers. Next, we examine how new techno
logies may allow the multiplex analysis of vast numbers of markers and how
computational methods such as artificial neural networks will provide meani
ngful interpretation of the data. In the near future, such an integrated ap
proach may provide a comprehensive prognostic tool for localized prostate c
ancer.