In this dissertation a systematic study of particle transport in tokamaks, using gyrokinetic simulations and theory, is presented. This work can be divided into three major parts. The first part studies particle transport in pure plasmas and investigates the origin and nature of flows against density gradients, also known as particle pinches. It is found that these pinches, which are primarily driven by temperature gradients, can also be responsible for the density peaking observed in experiments such as ASDEX-U, DIII-D or JET. The second part of this work studies plasmas with multiple ion species. First, we study helium ash transport and its effects in the core of a reactor plasma, finding that a helium pinch driven by finite toroidicity can be created in some cases. Second, we study deuterium and tritium plasmas from the point of view of isotope flow separation, finding that in a 50-50 deuterium-tritium plasma, a small fuel separation may occur. Finally, the last part studies the behavior of energetic species in reactor plasmas. It is found that alpha particles interact strongly with the background turbulence. Perhaps the most surprising finding is that the fluxes per particle of alphas can be stronger than the fluxes per particle of deuterium (i.e. main ion), as opposed to ``conventional wisdom'' which assumes that species with large gyroradii do not significantly interact with the turbulence.