The Gross-Pitaevskii equation (GPE) plays an important role in the description of Bose-Einstein condensates (BECs) at the mean-field level. The GPE belongs to the class of non-linear Schrodinger equations which are known to feature dynamical instability and collapse for attractive non-linear interactions. We show that the GPE with repulsive non-linear interactions typical for BECs features chaotic wave dynamics. We find positive Lyapunov exponents for BECs expanding in periodic and aperiodic smooth external potentials as well as disorder potentials. Our analysis demonstrates that wave chaos characterized by the exponential divergence of nearby initial wavefunctions is to be distinguished from the notion of non-integrability of non-linear wave equations. We discuss the implications of these observations for the limits of applicability of the GPE, the problem of Anderson localization, and the properties of the underlying many-body dynamics.