Multiphoton lithography (MPL) is a powerful and useful structuring tool capable of generating 2D and 3D arbitrary micro‐ and nanometer features of various materials with high spatial resolution down to nm‐scale. This technology has received tremendous interest in tissue engineering and medical device manufacturing, due to its ability to print sophisticated structures, which is difficult to achieve through traditional printing methods. Thorough consideration of two‐photon photoinitiators (PIs) and photoreactive biomaterials is key to the fabrication of such complex 3D micro‐ and nanostructures. In the current review, different types of two‐photon PIs are discussed for their use in biomedical applications. Next, an overview of biomaterials (both natural and synthetic polymers) along with their crosslinking mechanisms is provided. Finally, biomedical applications exploiting MPL are presented, including photocleaving and photopatterning strategies, biomedical devices, tissue engineering, organoids, organ‐on‐chip, and photodynamic therapy. This review offers a helicopter view on the use of MPL technology in the biomedical field and defines the necessary considerations toward selection or design of PIs and photoreactive biomaterials to serve a multitude of biomedical applications.