Molecular pathological epidemiology (MPE) is integrative molecular and population health science to address molecular pathogenesis and heterogeneity of disease processes. MPE of colon and rectal premalignant lesions (including hyperplastic polyps, tubular adenomas, tubulovillous adenomas, villous adenomas, traditional serrated adenomas, sessile serrated adenomas / sessile serrated polyps, and hamartomatous polyps) can provide unique opportunities to examine the influence of diet, lifestyle and environmental exposures on specific pathways of carcinogenesis. Colorectal neoplasia can provide a practical model where both malignant epithelial tumor (carcinoma), and its precursor, are subjected to molecular pathology analyses. KRAS, BRAF, and PIK3CA oncogene mutations, microsatellite instability, CpG island methylator phenotype, and LINE-1 methylation are commonly-examined tumor biomarkers. Future opportunities include comprehensive interrogation of genomics, epigenomics and pan-omics, as well as in vivo pathology analyses of tissue microenvironment, molecular networks and interactome by endomicroscopy. Considering the colorectal continuum hypothesis and emerging roles of gut microbiota and host immunity in tumorigenesis, detailed tumor location is important information. There are unique strengths and caveats, especially with regard to case ascertainment by colonoscopy. MPE of colorectal premalignant lesions can identify etiologic exposures associated with neoplastic initiation and progression, help us better understand colorectal carcinogenesis, and facilitate personalized prevention, screening, and therapy.