Evolutionary science provides evidence that diversity confers resilience. Yet, traditional multi-agent reinforcement learning techniques commonly enforce homogeneity to increase training sample efficiency. When a system of learning agents is not constrained to homogeneous policies, individual agents may develop diverse behaviors, resulting in emergent complementarity that benefits the system. Despite this feat, there is a surprising lack of tools that measure behavioral diversity in systems of learning agents. Such techniques would pave the way towards understanding the impact of diversity in collective resilience and performance. In this paper, we introduce System Neural Diversity (SND): a measure of behavioral heterogeneity for multi-agent systems where agents have stochastic policies. We discuss and prove its theoretical properties, and compare it with alternate, state-of-the-art behavioral diversity metrics used in cross-disciplinary domains. Through simulations of a variety of multi-agent tasks, we show how our metric constitutes an important diagnostic tool to analyze latent properties of behavioral heterogeneity. By comparing SND with task reward in static tasks, where the problem does not change during training, we show that it is key to understanding the effectiveness of heterogeneous vs homogeneous agents. In dynamic tasks, where the problem is affected by repeated disturbances during training, we show that heterogeneous agents are first able to learn specialized roles that allow them to cope with the disturbance, and then retain these roles when the disturbance is removed. SND allows a direct measurement of this latent resilience, while other proxies such as task performance (reward) fail to.