Technical Abstract: Although diet has been clearly associated with human health many potential mechanisms remain undefined. For instance, although the intestinal bacterial microflora has long been postulated to contribute to human health, little is known about the effects of diet on the bacterial microflora composition and the specific contributions of the microflora to human health. Thus, we analyzed 1) changes in the fecal microflora composition by fluorescent in-situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) and 2) changes in the fecal bile acid profile, in a crossover feeding study that investigated the effects of black tea drinking on blood lipids in hypercholesterolemic volunteers. DGGE analysis shows that each study subject harbors a specific bacterial profile that exhibits little change over time. Change from a 'free' living diet to the controlled study diet, or black tea drinking did not significantly change these bacterial profiles. FISH analysis revealed that even though black tea did not affect the specific bacterial groups that were analyzed, it did decrease the amounts of bacteria that were detected by the universal bacterial probe, but not by any of the specific probes. We did not detect any consistent effects of either diet or black tea drinking on the levels and proportions of fecal bile acids. Our results indicate that tea drinking affects some microflora components. Larger studies with well defined end points that control for the observed variation are needed to improve our understanding of the effects of diet on intestinal microflora and fecal bile acid profile.