Smoke emissions and particulate matter (PM) size distributions were investigated on a direct-injection (DI) single-cylinder diesel engine running on both gas-to-liquid (GTL) and diesel fuels utilizing a novel spiral-helical intake manifold design. Smoke opacity was measured at a wide range of engine loads and speeds with both fuels to examine the effect of using the new manifold on smoke emissions. In addition, total PM numbers of fine particles (PM diameter ≤ 1.0 μm) and coarse particles (˃1.0 μm) were quantified with both fuels. Moreover, high-resolution transmission electron microscopy (HRTEM) images were taken with different resolutions to observe the PM sizes produced from each fuel when using the new and normal manifolds. The results showed that using the novel manifold reduced smoke emissions for both GTL and diesel fuels with about 36% at low loads and 7% at high loads. However, using the new manifold with GTL fuel showed superior performance to reduce smoke with about 60% at low loads and 10% at high loads. For the PM size distribution, the new manifold reduced total PM emissions in general. However, significant reductions were obtained with fine PM sizes (0.3–1.0 μm) when GTL fuel was used with about 30% for constant load tests, and about 40% for constant speed tests. On the other hand, the new manifold tended to increase slightly the coarse PM sizes. The HRTEM images of the PM structure for both manifolds and fuels have confirmed the above results.