The lamina propria of colonic mucosa normally contains eosinophils, lymphocytes, plasma cells, and a few neutrophils. If the number of such cells is judged to be increased, colonic inflammation is said to be present. However, the number of cells present in normal mucosa has not been clearly established. Mild abnormalities are difficult to identify, yet might be associated with colonic dysfunction. We therefore developed a morphometric point-counting method to quantitatively analyze the areas occupied by different structures in the mucosa of the human colon. A computer was used to move a dot in a rectilinear pattern over the X400 magnified image of biopsy specimens obtained from throughout the colon by colonoscopy. The structure on which the dot landed was identified and tabulated by a pathologist. In preliminary studies, we established counting parameters that would yield the most representative results. Based on statistical analysis, it was decided to count 98 points in each of seven regions of six biopsy specimens, i.e., over 4000 points per subject. Results were expressed as percentages of counts landing on a given item, and represented the area of the biopsy specimen covered by that item. Using this method, we determined the range of normal in healthy volunteers. The sensitivity of this method was tested by studying patients with chronic diarrhea previously diagnosed as having or not having mild to moderate mucosal inflammation. In the patient group, colonic fluid absorption measured by a perfusion technique was directly correlated with epithelial cell counts and inversely correlated with lamina propria cellularity and with the counts of lamina propria neutrophils and plasma cells. We conclude that morphometric analysis of colon biopsy specimens can be used to quantitate histologic features of colonic mucosa and to accurately identify even mild abnormalities, and that it can be a useful clinical research tool.