Purpose: We evaluated the feasibility of biomarker development in the context of multicenter clinical trials. Experimental Design: Formalin-fixed, paraffin-embedded (FFPE) tissue samples were collected from a prospective adjuvant colon cancer trial (PETACC3). DNA was isolated from tumor as well as normal tissue and used for analysis of microsatellite instability, KRAS and BRAF genotyping, UGT1A1 genotyping, and loss of heterozygosity of 18 q loci. Immunohistochemistry was used to test expression of TERT, SMAD4, p53, and TYMS. Messenger RNA was retrieved and tested for use in expression profiling experiments. Results: Of the 3,278 patients entered in the study, FFPE blocks were obtained from 1,564 patients coming from 368 different centers in 31 countries. In over 95% of the samples, genomic DNA tests yielded a reliable result. Of the immmunohistochemical tests, p53 and SMAD4 staining did best with reliable results in over 85% of the cases. TERT was the most problematic test with 46% of failures, mostly due to insufficient tissue processing quality. Good quality mRNA was obtained, usable in expression profiling experiments. Conclusions: Prospective clinical trials can be used as framework for biomarker development using routinely processed FFPE tissues. Our results support the notion that as a rule, translational studies based on FFPE should be included in prospective clinical trials. (Clin Cancer Res 2009;15(17):5528-33) In spite of remarkable progress in our understanding of the molecular mechanisms involved in the development of cancer, the impact of this knowledge on cancer care has fallen short of expectations. Several reasons to explain this slow progress can be proposed. First adjuvant treatment, although rationally addressing the risk of recurrent disease, tends to be beneficial for a limited proportion of patients because it cannot be predicted who will recur or which recurring patient will respond to the adjuvant treatment. Biomarkers, capable of predicting recurrent disease as well as (non)response to adjuvant treatment modality, potentially provide a solution to this problem, as exemplified by the predictive value of c-Kit mutations for the response of GIST to the tyrosine-kinase inhibitor imatinib (1) or of KRAS mutations to epidermal growth factor receptor blocking agents (2, 3). Second, the long duration of clinical trials, which usually have outcome (disease free or overall survival) as end-point, hampers rapid introduction of new treatment modalities (4). Biomarkers indicating who responds would constitute surrogate study end-points that could be reached more rapidly (2).Few published putative biomarkers have made it into clinical practice because (a) most biomarker development studies were done on small patient numbers and significance in multivariate analysis was not studied or not confirmed; (b) often studies published are based on a learning set only, without independent validation on a test set; (c) most studies are retrospective and suffer from incomplete data or insufficient da...