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There is a clear trend toward the miniaturization of medical devices for minimally invasive medical procedures, ranging from diagnosis and targeted drug delivery to complex surgical interventions. Current research focuses on increasing the functionality of commercially successful capsule endoscope technology by developing active locomotion and telemetry. The size of such a capsule must not be larger than what a person can swallow without difficulty. One approach to increase functionality while still working within this size constraint is to build a modular robotic system in which the modules are swallowed one at a time, and the final assembly is performed inside the gastrointestinal (GI) tract. This paper addresses a fundamental challenge that must be be met for the success of such swallowable modular robots-their self-assembly. We propose to use magnets in a specific configuration on the mating faces of the modules. Our results show that high success rates can be achieved and snake-type robots can be self-assembled with compliant magnetic joints allowing them to adapt to highly irregular paths, such as the small intestine.