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Quantum key distribution protocols allow two honest distant parties to establish a common truly random secret key in the presence of powerful adversaries, provided that the two users share a short secret key beforehand. This pre-shared secret key is used mainly for authentication purposes in the post-processing of classical data that have been obtained during the quantum communication stage, and it prevents a man-in-the-middle attack. The necessity of a pre-shared key is usually considered to be the main drawback of quantum key distribution protocols, and it becomes even stronger for large networks involving more than two users. Here, we discuss the conditions under which physical unclonable functions can be integrated in currently available quantum key distribution systems in order to facilitate the generation and the distribution of the necessary pre-shared key with the smallest possible cost in the security of the systems. Moreover, the integration of physical unclonable functions in quantum key distribution networks allows for real-time authentication of the devices that are connected to the network.