There are vast numbers of bacteria present within the human colon and many studies have implicated these in CRC development. Despite this evidence, microbial diversity present at the mucosal surface has not been well characterised, with many investigations using culturing methods or extrapolating from analysis on faecal material. In this thesis, molecular analysis of colonic mucosal microbial diversity (caecum to rectum) in 10 healthy individuals revealed that each individual harboured their own microbial cohort that remained constant throughout the colon. Detailed 16S rDNA cloning and sequence analysis of caecal and rectal tissue from 1 individual reflected DGGE findings and showed the majority of sequences affiliated with the low G + C bacterial phylum, namely Clostridium cluster IV, XIVa and also the Bacteroides subphylum. DGGE and sequence analysis of a faecal sample from the same individual showed major differences in microbial diversity compared to tissue samples. DGGE analysis of paired neoplastic and adjacent normal mucosa samples revealed differences in microbial populations between the 2 tissues in a significant number of paired polyp samples. A number of cancer/normal tissue paired samples also displayed altered microbial diversity. Lectin immunohistochemistry was performed on selected healthy individuals and a number of paired neoplastic/normal colonic samples in order to determine host carbohydrate expression. Analysis of healthy tissue revealed individual glycosylation patterns, whilst neoplastic samples often showed altered glycosylation. Changes in host glycosylation did not appear to correlate with microbial diversity. RT-PCR was used to investigate gene expression of several fucosyltranferases in healthy individuals and selected neoplastic tissues. Downregulation in FUT3 expression was found in cancer tissue, correlating with loss of fucose-specific lectin staining in cancer tissue samples.