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The transport of suspensions of microparticles in confined environments is associated with complex phenomena at the interface of fluid mechanics and soft matter. Indeed, the deposition and assembly of particles under flow involve hydrodynamic, steric and colloidal forces, and can lead to the clogging of microchannels. The formation of clogs dramatically alters the performance of both natural and engineered systems, effectively limiting the use of microfluidic technology. While the fouling of porous filters has been studied at the macroscopic level, it is only recently that the formation of clogs has been considered at the pore scale, using microfluidic devices. In this review, we present the clogging mechanisms recently reported for suspension flows of colloidal particles and for biofluids in microfluidic channels, including sieving, bridging and aggregation of particles. We discuss the technological implications of the clogging of microchannels and the schemes that leverage the clog formation. We finally consider some of the outstanding challenges involving clogging in human health, which could be tackled with microfluidic methods.