The gut microbiome contributes to the variation of blood lipid levels, and secondary bile acids are associated with the effect of statins. Yet, our knowledge of how statins, one of our most common drug groups, affect the human microbiome is scarce. We aimed to characterize the effect of rosuvastatin on gut microbiome composition and inferred genetic content in stool samples from a randomized controlled trial (n = 66). No taxa were significantly altered by rosuvastatin during the study. However, rosuvastatin-treated participants showed a reduction in the collective genetic potential to transport and metabolize precursors of the pro-atherogenic metabolite trimethylamine-N-oxide (TMAO, p < 0.01), and an increase of related metabolites betaine and γ-butyrobetaine in plasma (p < 0.01). Exploratory analyses in the rosuvastatin group showed that participants with the least favorable treatment response (defined as < median change in high-density/low-density lipoprotein (HDL/ LDL) ratio) showed a marked increase in TMAO-levels compared to those with a more favorable response (p < 0.05). Our data suggest that while rosuvastatin has a limited effect on gut microbiome composition, it could exert broader collective effects on the microbiome relevant to their function, providing a rationale for further studies of the influence of statins on the gut microbiome. Originally discovered for their anti-microbial properties 1 , statins primarily reduce cholesterol levels and are first-line agents in the management of coronary artery disease (CAD) 2. The use of statins has been increasing rapidly in recent decades, and they are now one of the most commonly prescribed group of drugs in Western countries 2,3. The primary mode of action is inhibition of hydroxy-methyl-glutaryl-coenzyme A (HMG-CoA) reductase in the liver leading to decreased levels of low-density lipoprotein (LDL) cholesterol, but statins have other potential beneficial effects e.g., anti-inflammatory properties, inhibition of matrix metalloproteinases (MMPs) leading to plaque stabilization and inhibition of platelet aggregation 4. The mechanisms underlying these pleiotropic effects are not completely understood and may not necessarily be mediated through HMG-CoA reductase inhibition 5-7. Changes in the composition and function of gut microbiome have been implicated in the pathogenesis of a wide range of human conditions including various systemic disorders like cardiometabolic and autoimmune disorders 8,9. In cardiovascular disease (CVD), the gut microbiota-dependent metabolite trimethylamine-N-oxide (TMAO) and related metabolites, has been associated cardiovascular risk 8,9. The large intra-individual variation