Intrapellet H-2 and CO concentration gradients within catalyst pellets during Fischer-Tropsch (FT) synthesis lead to lighter and more paraffinic hydrocarbon products than when intrapellet diffusion limitations are negligible. These transport restrictions decrease both H-2 and CO concentrations near catalytic sites and lead to significant changes in product selectivity. Time-on-stream experiments show that after an experiment is started methane and paraffin/olefin ratios increase rapidly while CO conversion and C-5 + selectivity decrease on diffusion-limited pellets until steady state is reached. These changes are not observed on pellets free from transport limitations. Our results indicate that CO concentrations decrease continuously and to a greater extent than H-2 concentrations from the exterior to the center of large liquid-filled pellets. Extreme intrapellet diffusion restrictions totally deplete CO near the pellet center and restore the hydrogenolysis activity of Ru which is otherwise strongly inhibited by CO during FT synthesis. In the absence of CO, large hydrocarbons that are removed slowly from liquid-filled catalyst pores undergo extensive hydrogenolysis on Ru sites close to or at the center of the pellets, leading to lower wax yields and to higher methane and light paraffin selectivity.