In recent years, public health issues in the food industry have led to regulations concerning contaminants in foodstuffs, including coffee. Four main types of compound are known to contaminate coffee. First, pesticides come from agricultural treatments, transport and storage. Ochratoxin A is the main mycotoxin found in coffee and is linked to environmental conditions and post-harvest processing. Polycyclic aromatic hydrocarbon contamination can be of exogenous (during drying) or endogenous (during roasting) origin. Finally, acrylamide appears during roasting. This chapter discusses each of these compounds, reviewing our current state of knowledge, regulations for avoiding or dealing with contamination and effective ways of limiting contamination.