Abstract Background Pneumotosis cystoides intestinalis (PCI) is a rare condition characterised by the presence of intramural air or cystic lesions within the submucosa/subserosa of the small or large bowel (pneumatosis coli or PC). In the majority, it is an incidental finding and managed conservatively. Occasionally, it can create a dilemma regarding diagnosis, investigation and management. We present one such patient to illustrate this. Case report A 59-year old male presented as an emergency with abdominal pain. A CT KUB suggested free air surrounding the sigmoid colon? perforation. Following review, a subsequent contrast -CT confirmed PCI but no free peritoneal air. He was managed conservatively and discharged. He re-presented a few times to the ED with similar complaints and scans. He was then seen electively in a colorectal OPD and advised a colonoscopy and CT scan. This CT did not report the PCI. The colonoscopy was difficult, incomplete and consistent with PC with inflammation. Histology from cautiously taken biopsies was reported normal. Results On review in MDT, the need for investigating his symptoms versus serious concerns regarding a repeat colonoscopy and the relative contradiction to virtual CT colonoscopy were discussed. Finally, a qFIT test was performed, reported negative and the provisional diagnosis of IBS was reached, the patient reassured and discharged on conservative medical management. Conclusions This case highlights the rare condition of PCI and the various modes of presentation. It emphasises the importance of accurate CT diagnosis in the emergency setting and the use of qFIT to guide cautious elective colonoscopy/biopsies if indicated.