Bees are important pollinators that, because of extensive deforestation of their natural habitats, now forage widely in agricultural areas. This interaction with human agricultural activity has led to a reduction in the number of bee species because of contact with widely used pesticides. However, little is known about the adverse effects that exposure to such agents has on bee tissues and organs. In this review, we discuss the morphological alterations induced by environmental contaminants in the midgut and Malpighian tubules of bees; these two organs are involved in the absorption and excretion of toxic compounds, respectively. We also discuss the role of heat shock proteins, also known as stress proteins, in the cellular response to chemical compounds, and the importance of cell death as an indicator of the toxicity of these compounds. The analysis of these two cellular markers may be useful for monitoring bees that forage in agricultural areas.