Chronic and complex gut syndromes are complex to diagnose and manage, but good clinicopathologic correlation, recognition of new entities, understanding (and understanding the limits) of genetic susceptibility and the importance of the microbiome, dysbiosis and influence of the environmental allows development of new models for diagnosis. An awareness of overlap in chronic gut syndromes has been clarified by the realization that inflammatory pathways involved in chronic gut disease can arise through variable gene expression that is influenced by the environment in susceptible individuals. Recent advances in diagnosis of inflammatory bowel disease and diverticular disease may be aided by genetic tests but at present, pathology and some simple biomarkers such as C-reactive protein and fecal calprotectin are still mainstream investigative measures. When made aware of the importance of these recent developments in chronic gut disease, histopathologists can easily recognize colonic spirochetosis and microscopic colitis. The role of the microbiome alongside interaction with the environment, are now recognized as key players in complex diseases. Integration of appropriate and cost-effective tests into new paradigms will surely advance patients’ well-being and allow development of curative-targeted therapies rather than current treatments which, in many cases, merely alleviate symptoms.