Pretreatment refers to the process unit operation that is responsible for disrupting the naturally resistant structure of lignocellulosic biomass to provide reactive intermediates, such as sugars and sugar degradation products and so on, to biochemical or thermochemical processes for production of biofuels and bioproducts. Various promising pretreatment technologies have been developed through employing bench-scale pretreatment systems to obtain data that lead to new models and new insights on mechanisms, facilitating the development and commercialization of low-cost pretreatment technologies. However, the ability to design and select these systems in conjunction with bioprocessing of biomass a priori is limited, and detailed mass and heat transfer data are vital for the assessment and scale-up of these technologies. Batch reactors, including sealed glass reactors, tubular reactors, mixed reactors, microwave reactors and steam reactors, as well as continuous pretreatment systems such as flowthrough systems, have been widely applied to establish a fundamental understanding of pretreatment mechanisms, to investigate kinetics of thermochemical biomass deconstruction reactions, to provide process simulations for techno-economical assessments, and to improve reactor designs. This chapter discusses the applications and characteristics of different bench-scale pretreatment systems, mass and heat transfer in these systems, and the selection of bench-scale pretreatment systems.