The purpose of this study was to determine whether staining intensity in conjunction with the percentage of positive tumor cells should be used as an indicator of protein expression detected by immunohistochemistry. A tissue microarray of 1,197 colorectal cancers was immunostained for p53, Her2/neu, epidermal growth factor receptor (EGFR), adenomatosis polyposis coli (APC), and beta-catenin. Immunoreactivity was described by the percentage of positive tumor cells (percent positivity) and by the staining intensity (weak, moderate, strong). The interobserver reproducibility of both was evaluated by two pathologists. The association of T stage, N stage, tumor grade, vascular invasion, and survival with percent positivity, staining intensity, and the combination of both was assessed. In univariate analysis, protein expression assessed by percent positivity resulted in 11 significant associations between the proteins and clinico-pathological features. Eight of these 11 were also demonstrated using only the degree of staining intensity. However, more than half of the associations identified by percent positivity alone were lost when staining intensity was also analyzed in combination with the percentage of positive tumor cells. A scoring method based on percent positivity, rather than on staining intensity, for p53, Her2/neu, EGFR, APC, and beta-catenin is reproducible and appears to be sufficient for establishing associations of the selected tumor markers with most clinico-pathological features.