<b>Objective:</b> We hypothesized that a dietary combination of soy with either a probiotic (yoghurt) or a prebiotic (resistant starch) would result in enhanced lipid-lowering effects compared with a control soy diet, possibly via improvements in isoflavone bioavailability.<br><br><b>Subjects:</b> Mildly hypercholesterolaemic subjects (men and post-menopausal women) older than 45 years were recruited via the local media. Thirty-six subjects commenced the study; five withdrew.<br><br><b>Results:</b> Soy+probiotic significantly decreased total cholesterol (4.72.0%; P=0.038) and soy+prebiotic significantly decreased total and low-density lipoprotein cholesterol (5.51.6%; P=0.003 and 7.32.2%; P=0.005, respectively). The bioavailabilities of daidzein, genistein or equol were not affected by probiotic or prebiotic consumption or associated with lipid changes.<br><br><b>Conclusion:</b> Dietary combination of soy with either a probiotic or a prebiotic resulted in significant lipid lowering, not related to isoflavone bioavailability.<br>