In this paper, we present CHOMP (Covariant Hamiltonian Optimization for Motion Planning), a method for trajectory optimization invariant to reparametrization. CHOMP uses functional gradient techniques to iteratively improve the quality of an initial trajectory, optimizing a functional that trades off between a smoothness and an obstacle avoidance component. CHOMP can be used to locally optimize feasible trajectories, as well as to solve motion planning queries, converging to low- cost trajectories even when initialized with infeasible ones. It uses Hamiltonian Monte Carlo to alleviate the problem of convergence to high-cost local minima (and for probabilistic completeness), and is capable of respecting hard constraints along the trajectory. We present extensive experiments with CHOMP on manipulation and locomotion tasks, using 7-DOF manipulators and a rough-terrain quadruped robot.