The FHIT gene, a member of the histidine triad family has been identified as a tumor suppressor gene. Molecular genetic approaches to determine alterations in the FHIT gene in colorectal cancers have produced varying results with reported abnormalities of the FHIT gene transcripts in 13% to 50% of cases studied. FHIT has been reported to be involved in the regulation of apoptosis and cell cycle in cell culture systems. Immunohistochemical (IHC) studies of FHIT expression in human colon cancer and its correlation to apoptosis and clinical prognosis have been sparse. We studied 100 human colorectal cancers by IHC and a computerized image analysis (CIA) method to evaluate FHIT expression and the rate of apoptosis in tumors and corresponding mucosae. Follow-up data for at least five years was available for all patients. We correlated the results with tumor grade, stage and clinical prognosis. We used commercially available polyclonal anti FHIT antibody and Apoptaq kit on paraffin-embedded tumors and their corresponding mucosae and the SAMBA 4000 CIA system to evaluate the labeling index (LI), the mean optical density (MOD) of the stain and calculate a quick score (QS). The LI is the ratio of positively stained areas to the total area of the tissues examined, the MOD represents the concentration of the positive stain as measured per positive pixels and the QS a numeric product of the LI and MOD for each microscopic area examined. Image analysis of IHC staining of the tumor sections defined three main groups based on the reactivity of the anti FHIT polyclonal antibody. Group I included 23 cases where the LI was less than 55% with a mean of 36%. Eight cases in this group showed complete loss of FHIT expression. Group II included 41 cases where the LI was between 55% and 65% with a mean of 60%. Group III was composed of 36 cases where the LI was more than 65% with a mean of 69%. Our data showed that the absence or reduction of FHIT protein in the tumors, relative to morphologically normal mucosa, plays a role in the development of a few colorectal cancers (23%). Poorly differentiated carcinomas showed absent or decreased FHIT. A reduction of FHIT was positively correlated with the rate of distant metastases and worse prognosis. Over-expression of FHIT is directly proportional to the apoptotic rate in the tumors examined. CIA provides an objective and accurate assessment of the staining patterns and generates numerical data evaluating intensity better than depending on subjective light microscopy alone.