AimsVery early‐onset inflammatory bowel disease (VEO‐IBD) is a clinical umbrella term referring to IBD‐like symptoms arising in children before the age of 6 years, encompassing both ‘pure’ IBD, such as ulcerative colitis (UC) and Crohn's disease (CD) and monogenic diseases (MDs), the latter often involving genes associated with primary immunodeficiencies. Moreover, histological features in gastrointestinal (GI) biopsies in MD can also have IBD‐like morphology, making differential diagnosis difficult. Correct diagnosis is fundamental, as MDs show a more severe clinical course and their inadequate/untimely recognition leads to inappropriate therapy.Methods and resultsBiopsy samples from the lower and upper GI tract of 93 clinically diagnosed VEO‐IBD children were retrospectively selected in a multicentre cohort and histologically re‐evaluated by 10 pathologists blinded to clinical information. Each case was classified according to morphological patterns, including UC‐like; CD‐like; enterocolitis‐like; apoptotic; eosinophil‐rich; and IBD‐unclassified (IBD‐U). Nine (69%) MD children showed IBD‐like morphology; only the IBD‐U pattern correlated with MD diagnosis (P = 0.02) (available in 64 cases: 51 non‐MD, true early‐onset IBD/other; 13 MD cases). MD patients showed earlier GI symptom onset (18.7 versus 26.9 months) and were sent to endoscopy earlier (22 versus 37 months), these differences were statistically significant (P < 0.05). Upper GI histology was informative in 37 biopsies.ConclusionsThe diagnosis of the underlying cause of VEO‐IBD requires a multidisciplinary setting, and pathology, while being one of the fundamental puzzle pieces, is often difficult to interpret. A pattern‐based histological approach is therefore suggested, thus aiding the pathologist in VEO‐IBD reporting and multidisciplinary discussion.