We used real-time multiple particle tracking to quantitatively characterize the type and rates of transport of gene nanocarriers within live cells. The heterogeneous cytoplasmic transport of polyethylenimine (PEI)/DNA gene carriers was quantified by tracking their mean-square displacements over time and classified into active and nonactive transport populations on the basis of their effective diffusivities versus time. Nonactive gene carriers frequently displayed hop-diffusion trajectories, suggesting a porous cytoplasmic network of flexible biopolymers or sequential attachment and detachment events. Microtubule-dependent active transport of gene carriers resulted in an effective diffusivity 30-fold greater than that of nonactive carriers (at a time scale of 3 s). Compared to nonactive carriers in control cells with intact microtubules, microtubule depolymerization enhanced short-range motion of gene carriers but resulted in similar long-range transport. Multiple particle tracking characterizes gene carrier transport in complex biological environments and, therefore, may be a useful tool in quantifying rate-limiting steps in gene delivery within cells and other biological media.