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Molecular imaging in living systems has become an important tool for understanding molecular processes and cellular events in preclinical settings. It is also widely used for clinical applications such as early detection, localization, and characterization of diseases or for diagnostic purposes. Bioconjugation reactions are essential for preparing imaging agents as well as for labeling targeting molecules. The development of bioorthogonal chemistry has been of great interest for molecular imaging, allowing direct chemical functionalization of biological molecules in living cells and organisms in addition to improving chemical synthesis of imaging probes. In this chapter, chemical ligation methodologies applied for different imaging modalities such as optical, nuclear, and magnetic resonance imaging were reviewed, with a focus on bioorthogonal chemistry. Many imaging modalities have benefited from these biorthogonal reactions ranging from small-molecule modification for imaging probe development to selective labeling of biomolecules with an imaging agent in living animals, emphasizing versatility and broad application scope of bioorthogonal reactions.