Graph Neural Networks (GNNs) have been recently found to suffer from important limitations regarding their ability to capture the structure of the underlying graph. It has been shown that the expressive power of standard GNNs is bounded by the Weisfeiler-Lehman (WL) graph isomorphism test, from which they inherit proven limitations such as the inability to detect and count graph substructures. On the other hand, there is significant empirical evidence that substructures are often informative for downstream tasks, suggesting that it is desirable to design GNNs capable of leveraging this important source of information. To this end, we propose a novel topologically-aware message passing scheme based on subgraph isomorphism counting. We show that our architecture allows incorporating domain-specific inductive biases and that it is strictly more expressive than the WL test, while being able to disambiguate even hard instances of graph isomorphism. In contrast to recent works, our approach does not attempt to adhere to the WL hierarchy and therefore retains the locality and linear complexity of standard GNNs.