Soya proteins and isoflavones have been reported to exert beneficial effects on the serum lipid profile. More recently, this claim is being challenged. The objective of this study was to comprehensively examine the effects of soya consumption on the lipid profile using published trials. A detailed literature search was conducted via MEDLINE (from 2004 through February 2014), CENTRAL (The Cochrane Controlled Clinical Trials Register) and ClinicalTrials.gov for randomised controlled trials assessing the effects of soya on the lipid profile. The primary effect measure was the difference in means of the final measurements between the intervention and control groups. In all, thirty-five studies (fifty comparisons) were included in our analyses. Treatment duration ranged from 4 weeks to 1 year. Intake of soya products resulted in a significant reduction in serum LDL-cholesterol concentration, -4.83 (95% CI -7.34, -2.31) mg/dl, TAG, -4.92 (95% CI -7.79, -2.04) mg/dl, and total cholesterol (TC) concentrations, -5.33 (95% CI -8.35, -2.30) mg/dl. There was also a significant increase in serum HDL-cholesterol concentration, 1.40 (95% CI 0.58, 2.23) mg/dl. The I² statistic ranged from 92 to 99%, indicating significant heterogeneity. LDL reductions were more marked in hypercholesterolaemic patients, -7.47 (95% CI -11.79, -3.16) mg/dl, than in healthy subjects, -2.96 (95% CI -5.28, -0.65) mg/dl. LDL reduction was stronger when whole soya products (soya milk, soyabeans and nuts) were used as the test regimen, -11.06 (95% CI -15.74, -6.37) mg/dl, as opposed to when 'processed' soya extracts, -3.17 (95% CI -5.75, -0.58) mg/dl, were used. These data are consistent with the beneficial effects of soya proteins on serum LDL, HDL, TAG and TC concentrations. The effect was stronger in hypercholesterolaemic subjects. Whole soya foods appeared to be more beneficial than soya supplementation, whereas isoflavone supplementation had no effects on the lipid profile.