Due to their increased cancer risk, patients with longstanding inflammatory bowel disease (IBD) are offered endoscopic surveillance with concomitant histopathological assessment, aimed at identifying dysplasia as a precursor lesion of colitis-associated colorectal cancer. However, this strategy is beset with difficulties and limitations. Recently, a novel classification criterion for colitis-associated low-grade dysplasia (LGD) has been proposed and an association between non-conventional dysplasia and progression reported, suggesting the possibility of histology-based stratification of patients with colitis-associated lesions. Here, a cohort of colitis-associated lesions was assessed by a panel of six experienced pathologists to test the applicability of the published classification criteria and to try and validate the association between non-conventional dysplasia and progression. While confirming the presence of different morphological patterns of colitis-associated dysplasia, the study demonstrated difficulties concerning diagnostic reproducibility between pathologists and was unable to validate the association of non-conventional dysplasia with cancer progression. Our study highlights the overall difficulty of using histological assessment of precursor lesions for cancer risk prediction in IBD patients and suggests the need for a different diagnostic strategy that can objectively identify high-risk phenotypes.