Autonomous systems promise solutions to a wide range of technical and societal problems, and their use appears especially attractive in safety-critical domains, like transportation or factory automation. This paper focuses on an underestimated aspect of autonomous systems: their security implications. Many approaches to design traditional secure systems do not readily transfer to autonomous systems, due to their high complexity and exposure to a broad spectrum of threats. Moreover, autonomous systems are often designed to be extremely long-living, and any security solutions should anticipate future threats to some extent. This paper starts with an overview of security threats applicable to autonomous systems and today's countermeasures to address these threats. Then, two representative techniques are elucidated in more detail: the use of post-quantum cryptography to achieve secure communication, and remote attestation as one essential building block for platform security.