4107 Background: Treatment resistance and the lack of reliable prognostic factors are major obstacles in rectal cancer (RC) management. A blind screening of RC transcriptome changes after chemoradiotherapy (CRT) could pinpoint proteins potentially involved in CRT resistance. Evaluation of their relation with disease outcome could help to identify novel therapeutic and prognostic candidates. Methods and Results: In a first stage we screened dynamic changes of RC transcriptome after CRT using blind and directed strategies. On one side, we selected fresh RC samples, before and after CRT, from three uT3N0 patients with poor response, as assessed by Dworak´s TRG2 and minimal downstaging (ypT2–3N0). Serial Analysis of Gene Expression (microSAGE) was conducted, six libraries were generated, sequencing around 30.000 tags. MonteCarlo analysis of dynamic “intra-patient” changes, and “inter-patient” comparisons revealed a set of 25 genes with shared significant changes. On another side, a collection of 29 genes was selected from the literature, In a second stage we evaluated dynamic changes in the mixed set of 54 genes in a cohort of 125 stage II-III RC patients treated with preopCRT. Samples from 74 patients assured sufficient tumor quality and quantity before and after CRT. mRNA dynamic changes of gene expression were evaluated by TaqMan Low Density Arrays (TLDAs), and statistical analysis done by Wilcoxon test with bootstrap and regulated genes selected for discriminant and Cox proportional-hazards regression analysis. Induction of mRNA TFF3, screened in the blind phase SAGE and exhibiting important tumor promotion and progression functions, was associated with tumor relapse and shorter survival. Also, analysis of TFF3 immunohistochemical expression in surgical samples revealed that an on/off pattern of intraluminal gland expression (PAS independent) strongly predicted tumor relapse. Conclusions: Upregulation of TFF3 after CRT, and an easily determined IHC pattern, predicted RC relapse in preoperatively treated patients. Confirmatory prognostic studies in independent series should be conducted, and its potential therapeutic merits as a candidate target evaluated. No significant financial relationships to disclose.