Chromosome 18q allelic loss has been reported to have prognostic significance in stage II colorectal carcinoma. We have developed a fluorescent multiplex polymerase chain reaction assay to analyze five microsatellite markers (D18S55, D18S58, D18S61, D18S64, and D18S69) for allelic loss at the long arm of chromosome 18. Amplicon detection and evaluation was accomplished by capillary electrophoresis using an ABI 310 genetic analyzer. Robustness of the assay when performed on DNA extracted from formalinfixed, paraffin-embedded tissue sections was confirmed by analyzing its repeatability and reproducibility. Allelic loss was assessed in 61 stage II colorectal tumors and was detected in 58% (31 of 53) of tumors not showing instability. As part of the study, results of 207 previous polymerase chain reaction/polyacrylamide-based assays were re-evaluated by two independent observers to determine the degree of concordance of visual evaluation. In the case of stage II colorectal tumors, when electropherogram results were compared with those obtained from visual evaluation of the same markers after polyacrylamide gel electrophoresis, discrepancies between observers were detected in 16.4% of determinations. In conclusion, we have developed a robust and reliable assay for multiplexed loss of heterozygosity determination that improves assessment of chromosome 18q allelic loss in colorectal tumors processed as routine formalin-fixed, paraffin-embedded specimens. The prognosis of colorectal cancer is mainly based on tumor stage at time of diagnosis. However, other clinicopathological features such as tumor location, perineural invasion, lymphatic vessel invasion and differentiation, as well as certain molecular alterations such as microsatellite instability, have also been reported to be predictors of tumor recurrence and patient outcome. 1,2 Survival for patients with tumors confined to the muscularis propria (stage I) or with extensive metastatic disease (stage IV) is predictable; however, tumor biological behavior after surgical treatment for stage II and III tumors is not well established. Approximately 30% of patients with stage II colon cancer will relapse and die of the disease. [3][4][5][6] More significantly, up to 65% of patients with stage III tumors will succumb to colon cancer. The use of adjuvant therapies in patients with stage II lesions is not exempt of controversy. These therapies have sideeffects, and should be given to those patients who would benefit from them. 7 Prognostic markers that complement standard clinical and pathological staging further stratify stage II patients into high-risk and lowrisk groups of relapse after surgery, and better guide adjuvant therapy. Biological factors that account for the different outcome among patients presenting with the same clinical stage are still poorly understood, but several studies have revealed the prognostic significance of 18q allelic loss in stage II colorectal carcinomas. 3,5,6,8 -10 Loss of this region, from which several tumor suppressor genes have been c...