Metal-organic frameworks (MOFs) are a very promising platform for applications in various industries. In recent years, a variety of methods have been developed for the preparation and modification of MOFs, providing a wide range of materials for different applications in life science. Despite the wide range of different MOFs in terms of properties/sizes/chemical nature, they have not found wide application in biomedical practices at present. In this review, we look at the main methods for the preparation of MOFs that can ensure biomedical applications. In addition, we also review the available options for tuning the key parameters, such as size, morphology, and porosity, which are crucial for the use of MOFs in biomedical systems. This review also analyses possible applications for MOFs of different natures. Their high porosity allows the use of MOFs as universal carriers for different therapeutic molecules in the human body. The wide range of chemical species involved in the synthesis of MOFs makes it possible to enhance targeting and prolongation, as well as to create delivery systems that are sensitive to various factors. In addition, we also highlight how injectable, oral, and even ocular delivery systems based on MOFs can be used. The possibility of using MOFs as therapeutic agents and sensitizers in photodynamic, photothermal, and sonodynamic therapy was also reviewed. MOFs have demonstrated high selectivity in various diagnostic systems, making them promising for future applications. The present review aims to systematize the main ways of modifying MOFs, as well as the biomedical applications of various systems based on MOFs.