Learning workable representations of dynamical systems is becoming an increasingly important problem in a number of application areas. By leveraging recent work connecting deep neural networks to systems of differential equations, we propose variational integrator networks, a class of neural network architectures designed to preserve the geometric structure of physical systems. This class of network architectures facilitates accurate long-term prediction, interpretability, and data-efficient learning, while still remaining highly flexible and capable of modeling complex behavior. We demonstrate that they both noisy observations in phase space and from image pixels within which the unknown dynamics are embedded.