Aims: A wide spectrum of well-differentiated neuroendocrine proliferations (NEPs) are observed in inflammatory bowel disease (IBD), ranging from neuroendocrine tumours (NETs) to microscopic neuroendocrine cell clusters, best described as neuroendocrine cell micronests (NCMs). Finding NCMs in surveillance biopsies of IBD patients often poses a diagnostic conundrum. While such lesions may have been referred to as ‘microcarcinoids’ in the literature, it is unclear whether these represent early neoplasms. The study was undertaken to characterise NCMs and to differentiate NCMs from NETs. Methods and results: Institutional surgical pathology archives were searched to identify cases of NEPs in IBD patients. Clinicopathological features were examined. NCMs were defined as scattered, indistinct neuroendocrine cell clusters without confluent growth or new stroma formation, located in the lamina propria and muscularis mucosae. NETs were defined as discrete, mass-forming lesions. Seventeen NEPs were identified, including eight NCMs and nine NETs. All NEPs were incidentally discovered. While NETs were commonly found in the rectum and appendix, NCMs were only noted in the rectosigmoid area. Unlike NETs, NCMs could not be measured as a discrete lesion as these clusters were non-confluent and scattered. None of the patients with NCMs developed NETs after a mean follow-up of 4.1 years (range = 0.5–21.0 years). None of the NETs showed NCMs in the background mucosa. Conclusions: NCMs have distinct pathological features, are not associated with NETs in IBD patients and should not be misinterpreted as ‘microcarcinoids’. Identification of NCMs in surveillance biopsies may not require further clinical work-up or invasive procedures usually performed for NETs.