The pores in metal-organic frameworks (MOFs) can be functionalized by placing chemical entities along the backbone and within the backbone. This chemistry is enabled by the architectural, thermal, and chemical robustness of the frameworks and the ability to characterize them by many diffraction and spectroscopic techniques. The pore chemistry of MOFs is articulated in terms of site isolation, coupling, and cooperation and relate that to their functions in guest recognition, catalysis, ion and electron transport, energy transfer, pore-dynamic modulation, and interface construction. It is envisioned that the ultimate control of pore chemistry requires arranging functionalities into defined sequences and developing techniques for reading and writing such sequences within the pores.