Covalent organic frameworks (COFs) are crystalline porous organic structures with two-or three-dimensional (2D or 3D) features and composed of building blocks being connected via covalent bonds. The manifold applications of COFs in optoelectronic devices, energy conversion and storage, adsorption, separation, sensing, organocatalysis, photocatalysis, electrocatalytic reactions, and biomedicine are increasing because of their notable intrinsic features such as large surface area, porosity, designable structure, low density, crystallinity, biocompatibility, and high chemical stability. These properties have rendered 2D and 3D COF-based materials as desirable entities for drug delivery, gene delivery, photothermal therapy, photodynamic therapy, combination therapy, biosensing, bioimaging, and anticancer activities. Herein, different reactions and methods for the synthesis of 2D and 3D COFs are reviewed with special emphasis on the construction and state-of-the-art progress pertaining to the biomedical applications of 2D and 3D COFs of varying shapes, sizes, and structures. Specifically, stimuli-responsive COFs-based systems and targeted drug delivery approaches are summarized.