In this review, the nature and impact of progress in the study of mucins is outlined, emphasizing the current understanding of the structure and physiological function of these molecules in the colorectum. The use of new methods for preparation and separation has led to improvements in the analysis of mucins; these are detailed, as are their difficulties and pitfalls. Results obtained with these methods are correlated with long-established histochemical techniques and the use of chemical, lectin, and antibody reagents for general and specific detection of mucins in all procedures is described. Improvements in the detection and analysis of mucins in biopsy-size tissue samples and in larger numbers of individual clinical cases have now permitted a much wider approach to the pathological evaluation of mucin biology and progress with these techniques is outlined. The significance of the discovery of a family of mucin genes is presented and new concepts of mucin structure resulting from these studies are described. Bacterial degradation of the mucus layer at the surface of the colorectal mucosa is considered in line with the homeostatic relationship with mucosal mucin synthesis. Finally, the implications of abnormal mucins in colorectal disease are considered in the light of recent methodological advances.