The aim of this study was to investigate the presence of microaggregates of macrophages (CD- 68 positive cells) in macroscopically normal buccal mucosa in patients with inflammatory bowel disease (IBD). Fifty two patients with clinically and pathohistologically diagnosed IBD, thirty patients with Crohn’s disease (CD), twenty two patients with ulcerative colitis (UC), and twenty five controls, matched for sex and age, were involved. The occurrence of CD-68 positive cells microaggregates was more frequent in CD patients comparing with UC patients (P = 0.0093), and the controls (P = 0.0001) respectively. There was no statistically significant difference in occurrence of CD-68 positive microaggregates in patients with positive microbiological findings (P = 0.8258). The results suggest that microaggregates of macrophages are more frequently present in apparently normal buccal mucosa in patients with CD than in patients with UC independently of microbiological findings. Therefore, it could be a potential marker for differentiating patients with Crohn’s disease from UC patients, when standard tools failed. (doi: 10.5562/cca1779)