We conducted a comprehensive evaluation of serum protein patterns in an effort to identify biomarkers for colon tumors. In the first step of the experimental procedures we screened sera from 32 healthy controls and 58 sera of patients with colorectal malignancy using SELDI-TOF mass spectrometry. The analysis of the discovery set therefore suggested that serum profiling using SELDI-TOF MS identifies protein peaks that allow the discernment of patients with colorectal malignancy from control individuals in our collection of sera. To exclude fortuitous separation of the malignant samples from healthy controls in the discovery set, the predictive value of the 8941.1 Da peak was then tested with an independently collected, blinded validation set consisting of 59 samples. Thirteen of the 59 samples (22.0%) received an unknown classification, i.e., the peak values were between the upper and lower thresholds. Fourty-five of the remaining 46 samples were correctly classified (sensitivity=96.9% and specificity=100%). We therefore proceeded with protein identification of the most prominent features. We identified complement C3a-desArg at the peaks with m/z of 8941.1 and 9148.7 (the peak at 9148.7 is the expected satellite peak of C3a-desArg and reflects the sinapinic acid adduct caused by matrix-assisted ionization). C3a-desArg is the stable form of C3a in serum. We next wished to confirm the SELDI-TOF MS based results using an independent method for protein quantification. Serum levels of complement C3a-desArg were assessed using a commercially available ELISA test. In summary, our results show that SELDI-TOF MS based serum protein profiling reveals certain m/z values that allow discernment of sera from patients with and without colorectal cancer. The subsequent protein identification revealed complement C3a-desArg as the determining protein that allows prediction of the presence of malignant colorectal disease with a sensitivity of 96.8% and a specificity of 96.2%. The marker also proved useful when applied to an additional independent sample set consisting of sera from patients with colorectal adenomas, in which 86.1% of the adenoma samples revealed serum levels of complement C3a-desArg above the previously determined threshold for cancer samples, 8.3% were undetermined, and only 5.6% were classified as normal.