Colorectal cancer is one of our most common malignancies and the second leading cause of cancer death worldwide. About 1/3 of the tumors are located in the rectum. Treatment advances such as the introduction of the standardized surgical technique total mesorectal excision (TME), pre-operative radiotherapy, and adjuvant chemotherapy have reduced the previously high local recurrence rates and improved survival in rectal cancer patients, but despite these advances about 40% of the patients still die from disseminated disease. Rectal cancer evolves through an accumulation of genetic alterations in the tumor cells, and although multiple such changes have been characterized, the molecular markers have not yet gained widespread clinical use. The prognostic markers currently available fail to identify patients at risk for tumor recurrencies, which implies a need for refined prognostic tools. This thesis focuses on analysis of different molecular events in rectal cancer with correlations to prognosis. Papers I-II evaluate the novel serological markers suPAR and TIMP-1 analyzed in pre-treatment plasma samples from patients with rectal cancer. High suPAR and TIMP-1 values were associated with shorter survival and these markers may thus be of potential prognostic use. In paper III, we evaluated the tissue microarray technique (TMA) for immunohistochemistry (IHC) using the markers p53 and Ki-67. Good quality staining was obtained and TMA could reproduce the results obtained from whole-tissue sections. Paper IV presents IHC tumor profiling using TMA in rectal cancer with correlations to prognosis using the markers Ki-67, p53, Bcl-2, EGFR, ß-catenin, E-cadherin, MLH1, and MSH2. The cell adhesion molecules ß-catenin and E-cadherin significantly correlated with metastatic disease, whereas the other markers did not. In paper V, we studied 30 cancers from patients younger than 50 years at diagnosis with respect to molecular alterations associated with the microsatellite instability (MSI) and the chromosomal instability (CIN) pathways for colorectal cancer development. We found that microsatellite stable (MSS), aneuploid tumors with increased expression of p53 and ß-catenin predominate also among young rectal cancer patients. Only 10% of the tumors displayed MSI, all of which showed loss of expression for MSH2, which suggests presence of a mutation associated with hereditary nonpolyposis colorectal cancer (HNPCC). In summary, this thesis presents confirmatory data on the plasma levels of suPAR and TIMP-1 as presumptive prognostic markers in rectal cancer. In addition, we have demonstrated that the TMA-technique allows high-throughput immunostaining in rectal cancer. A TMA-based molecular profiling demonstrated that aberrant expression patterns frequently occur, and that the expression of the cell-adhesion proteins ß-catenin and E-cadherin correlated with clinical outcome. Finally, the 5% of the rectal cancers that occur in young patients predominantly develop through the CIN pathway, whereas MSI is found in a small, HNPCC-related subset of the tumors. Hence, other mechanisms than defective MMR and HNPCC cause rectal cancer in the majority of young patients