Owing to their unusual geometry and polarity, neurons face a tremendous transport challenge. In particular, the bi-directional movement of many cargoes between cell body and synapse that takes place within extremely long, narrow axons requires motor-driven active transport along polarized microtubules. We summarize some imaging and theoretical modeling strategies recently developed to better understand axonal transport and neuronal function. Our approaches are motivated by three questions: (1) Can we predict the response of a complex trafficking system to perturbations of various components, either alone, or in combination? (2) What is the relationship between in vitro measurements of single motor properties and the movement of motor-cargo complexes in vivo? (3) What key principles govern the operation of the neuronal transport system? We discuss the imaging of vesicular transport in Drosophila melanogaster larval axons, and the development of quantitative schemes to define transport function via the extraction of kinematic parameters from these images. The application of these schemes to images from wild-type larvae and larvae expressing mutations in specific transport proteins allows rigorous quantification of transport kinematics in functional and dysfunctional neurons. Finally, we present some strategies and results for the theoretical modeling of axonal transport, and discuss the integration of these results with experimental data.