Abstract Indomethacin is a widely used nonsteroidal antiphlogistic compound used—among others—for the treatment of rheumatoid arthritis in humans. Common side effects of indomethacin in the gastrointestinal tract include ulcerative lesions and petechial bleeding in the mucosa. In the rat, oral intake of indomethacin induces ulcerations in the mucosa of the stomach and, if administered systemically, edema, petechial bleeding, and ulcerations in the small intestine. In order to determine if systemic administration of indomethacin may induce changes in villous perfusion, we assessed the effect of indomethacin on erythrocyte velocity and the diameter of the main arteriole in the villi of the rat ileum. We found that indomethacin led to a significant decrease in mean arteriolar blood flow (6.3 ± 0.8 vs 5.0 ± 1.2 nl/min, means ± SD) 7 days after administration. Mean diameter of the main arteriole remained unchanged (control, 7.8 ± 0.8 vs indomethacin, 7.0 ± 0.9 μm). In conclusion, systemic application of indomethacin leads to a decrease in blood supply to the mucosa. We previously found an increase in villous perfusion when assessed 24 h after administration of indomethacin, accompanied by an increase in arteriolar diameter of the main arteriole. In summary, different regimens of application of indomethacin lead to varying observations in microcirculatory parameters in single villi. Further studies are required to identify the underlying mechanisms.