Subcellular microcompartments, consisting of multienzyme complexes embedded within the cellular, highly viscous matrix, associated with the cytoskeleton, or situated along membranes, are operating according to exclusion principles and favor preferred pathways of intermediates. This process, called metabolite or substrate channeling, is defined as transfer of intermediates between sequential enzymes without equilibration of these metabolites with the surrounding bulk solution. Such an association between two or more sequential enzyme or transport reactions in a microcompartment, forming a distinct functional pool of intermediates, is also called functional coupling. It can be considered as a general mechanism to increase efficiency of sequential reactions in a metabolic pathway. As metabolite channeling leads to segregation of a metabolic pathway from other cellular reactions, it represents a specific kind of metabolic compartmentation similar to that operating within membrane-separated organelles or by restricted two-dimensional diffusion at surface boundary layers. Here, metabolite channeling is described with special emphasis on high-energy phosphate channeling by creatine kinase (CK), the phosphocreatine circuit or shuttle, and the mitochondrial CK (MtCK) isoenzyme.