Counting immunoglobulin (Ig)-containing cells in colonic mucosal biopsies can help to objectively support the differential diagnosis of ulcerative colitis and Crohn's disease. Before a method for counting Ig-containing cells can be applied in a clinical setting, however, its reproducibility must be determined. This study investigated the reproducibility of two different methods for counting such cells. The use of a light microscope with an ocular grid resulted in a slightly better reproducibility than did the use of a projection microscope with a graphics tablet. Moreover, the ocular grid method had a higher efficiency. The counting of IgM- and IgG-containing cells had a considerably higher reproducibility than did the counting of IgA-containing cells. To determine the minimal number of cells to be counted in order to ascertain a stabilized mean number of Ig-containing cells, the running means of counts of Ig-containing cells were calculated for two observers. When at least 600 Ig-containing cells (i.e., two to four fields) were counted, the interobserver variation of the running means was less than 10% for IgA and IgG counts and less than 5% for IgM counts. Since earlier studies showed differences in the counts of IgA-, IgG- and IgM-containing cells between ulcerative colitis and Crohn's disease to be, respectively, 3%, 25% and 28%, the results of the present study suggest that the proposed counting method can be useful in the differentiation between these entities.