Fermentation products, SCFA, particularly butyrate, are considered a sign of ‘good’ bowel health but the influence of bacterial population composition and diet on inter-individual difference in metabolites and colonic health is poorly understood. Faecal specimens were collected weekly from eight healthy human volunteers over 12 weeks. Dietary intake was self-reported and ten macronutrient factors were analysed at selected weekly periods. Faecal weight, pH and moisture were recorded, and SCFA concentrations were measured in all samples. From each specimen, DNA was prepared and eubacterial 16S rRNA gene PCR performed. Bacterial population profiles were captured by denaturing gradient gel electrophoresis (DGGE) of PCR products, and multivariate statistical analysis was performed. Faecal weight, pH and moisture varied widely within and between individuals. Average total SCFA concentrations over 12 weeks ranged from 36·9 to 144·4 mmol/kg in 48 h specimens and faecal butyrate concentrations ranged from 1·8 to 48·5 mmol/kg. Two individuals with butyrate concentrations below 10 mmol/kg were considered to be ‘low butyrate types’ and may represent an at-risk population for bowel health. Dietary fat, sugar and carbohydrate showed weak correlation with SCFA (R − 0·612, P = 0·015; R 0·607, P = 0·016; R 0·610, P = 0·016, respectively) and butyrate concentrations (R − 0·593, P = 0·02; R 0·504, P = 0·054; R 0·528, P = 0·043, respectively). Multivariate analysis of DGGE bacterial profiles demonstrated concise and repeated grouping of intra-individual samples, but these were combined with distinct inter-individual differences (analysis of similarities P < 0·001, R ≥ 0·99) The exact relationship of these SCFA values to the overall bacterial profiles and SCFA-producer bacterial groups was not direct nor linear.