This study evaluated the effects of soy protein containing isoflavones on the lipid profile of women. A meta-analysis including 13 eligible randomized controlled trials was carried out. The literature was systematically searched for randomized controlled trials on the effects of soy protein containing isoflavones on the serum lipids of adult women. The main searched databases were PubMed, Cochrane Library, MedLine, Lilacs and Web of Science. Randomized controlled trials were included if they met the following criteria: published from 1966 to 2005, the study population consisted of women only, had either a crossover or a parallel design and the amounts of soy protein and isoflavones consumed were provided. Weighted mean effect sizes were calculated for net changes in serum lipid concentrations using fixed-effects and random-effects models. Prespecified subgroup analyses were performed to explore the influence of covariates on net lipid change. Soy protein with isoflavones was associated with a significant decrease in total serum cholesterol (by 5.34mg/dL, or 2.4%, p=0.03). No significant associations were detected for low density lipoprotein-cholesterol, triacylglycerols and high density lipoprotein-cholesterol. Amounts of soy protein greater than 40g decreased total cholesterol by 6.56mg/dL (95% CI: -12.35 to -0.39, p=0.04). Soy protein supplementation had small statistically significant effects on the total serum cholesterol of women, but they were clinically insignificant. Furthermore, there were no statistically significant effects on serum low density lipoprotein-cholesterol, high density lipoprotein-cholesterol or triglycerides.