Solid cancers arise as a consequence of the accumulation of genetic and epigenetic alterations within a single cell or group of cells. Their ongoing characterization is providing a range of acid-based molecular markers for neoplasia. This, together with continuous refinements to the polymerase chain reaction (PCR), had led to the emergence of PCR-based assays as potential aids in the clinical management of cancer patients. Although the sensitivity of molecular diagnosis has the potential to aid clinicians in therapeutic decision making, problems with its specificity mean that the predictive value of molecular staging is still unproved. Its role in the identification of minimal residual disease after curative surgical resection requires clinical validation in further prospective studies.