Keywords: secondary progressive multiple sclerosis; cholesterol; simvastatin. and a faster decline in serum cholesterol levels (all p <0.05), when compared with placebo.The cholesterol-independent model, in which simvastatin has a direct effect on the clinical outcome measures and brain atrophy, independent of its impact on lowering the serum cholesterol levels, was the more likely model. When we deconstructed the total treatment effect on EDSS and block design, into indirect effects, which were mediated by brain atrophy, and direct effects, brain atrophy was responsible for 31% of the total treatment effect on EDSS (beta=-0.037, 95% credible interval [CI]=-0.075, -0.010), and 35% of the total treatment effect on block design (beta=0.33, 95%CI=0.06, 0.72). The effect of simvastatin on both outcomes was independent of serum cholesterol levels (EDSS: beta=-0.139, 95% credible interval=-0.255,-0.025; brain atrophy: beta=0.32, 95% credible interval=0.09,0.54).The effect of simvastatin on disability and cognitive worsening is partially mediated by brain atrophy but is independent of cholesterol reduction. Our mechanistic approach can be applied to other medications to elucidate the pathways underlying treatment effects in progressive MS.