Background Systemic mastocytosis is a rare disease and most patients have pigmented urticarial skin lesions. It can be easily missed and misdiagnosed in small biopsies, especially in those patients with nonspecific clinical complaints or untypical skin lesions. Case presentation We report a case of 69-year-old man who have presented with 2-year of diarrhea, progressive weight loss of 20kg and abdominal distention for 3 months. Ultrasound and abdominal CT scan showed massive effusions in abdominal and pelvic cavity. Colonoscopy was performed and showed intensive mucosal proliferations forming polypoid appearances. Microscopically, monotonously uniform, small, round tumor cells with slightly rich cytoplasm were concentrated between the residual glands in the colonoscopic biopsy. The tumor cells showed positive expression of CD117 and S-100, and low Ki-67 proliferation index of 2%, while Trypsin, CK, CD68, CD1a, Langerin, Syn, CgA, CD56, SATB2, CD20, CD3, α-inhibin and SMA were all negative. KIT D816V mutation was detected as well. Liver biopsy showed that CD117 positive cells were more than 15 cells in aggregates around the hepatic portal area and less than 15% mast cells were found in bone marrow smears. No multiple or diffuse pattern of mast cells infiltration was seen by repeated skin biopsies of skin lesions. With all these considered, the diagnosis of aggressive systemic mastocytosis was made. Conclusions The diagnosis of aggressive systemic mastocytosis is challenging for untypical clinical manifestations and subtle or inconspicuous lesions, especially in endoscopic biopsies, which requires awareness and a close teamwork of pathologists and clinicians.