We set out to compare the effect of diets containing intact seeds as food ingredients on colon function and fermentation-dependent events. Using a randomized cross over design, twelve healthy adults were recruited and required to consume an experimental diet containing intact or ground seeds for 7-days then after returning to their usual diet for 21-days to consume the second experimental diet for 7-days. All foods consumed during the experimental dietary periods were supplied by the researchers. Stools passed on three consecutive days on the usual diet prior to commencement and on days 5, 6 and 7 during each experimental diet, were collected. Outcome measures were whole gut transit time, 24 h stool output, faecal pH, particle size, and short chain fatty acid content. Seeds recovered from stools were examined by scanning electron microscopy. Nine of the twelve subjects completed all aspects of the study. Consumption of intact seeds compared to ground seeds increased 24 h faecal wet weight (mean 258 g +/- 123 g and 170 g +/- 63 g, respectively; P=0.005) and dry weight (78 g +/- 34 g and 46 g +/- 28 g, respectively; P=0.003). Whole gut transit times and moisture content of stools were not different. There was a trend for stools from the whole seed diet to be more acidic than those from the ground seed diet (pH 6.2 +/- 0.3 and pH 6.6 +/- 0.3, respectively; P=0.06) and they contained more short chain fatty acids (35 +/- 5.2 and 30 +/- 10.5 mmol/kg, respectively; P=0.05). Large amounts of apparently whole seeds were recovered from stools, but internally the endosperm was often eroded and coated with bacteria. Intact seeds as food ingredients bring about changes to the colonic environment and to faecal composition that may reduce the risk of colon cancer.