Modular microrobots will enable exploration and manipulation in tiny and difficult to access spaces. Modularity allows reconfiguration for adaptation to unstructured environments. In addition, individual modules can be designed for simple specific functions, thereby reducing fabrication complexity and easing downscaling. For modular microrobots, a robust connection mechanism is indispensable. In this paper, we introduce a magnetic self-aligning hermaphroditic connector. Self-alignment is achieved by a specific magnetic design that creates an attractive force, as well as a torque that aligns the mating faces into a known configuration. Each mating face is identical, and this hermaphroditic design, combined with selfalignment, provides a priori knowledge that once a mechanical connection is established, the intramodular communication system is also functional. Experiments with upscaled models demonstrate robust self-alignment and the desirable characteristics of the communication system. The use of magnets for the mechanical connection is the key for the scalability of the connector, as geometrical downscaling is favorable for magnet-magnet interaction and no moving parts are required. The analysis presented here will enable an optimal design of microscaled connectors.