In Japan, maximum residue limits for pesticides (MRL) in coffee are set on green coffee beans, but not roasted coffee beans, although roasted beans are actually used to prepare coffee for drinking. Little is known about the behavior of pesticides during the roasting process. In the present study, we examined the changes in the concentration of pesticide (organochlorine: γ-BHC, chlordane and heptachlor) residues in coffee beans during the roasting process. We prepared green coffee beans spiked with these pesticides (0.2 and 1.0 μg/g), and the residue levels in the beans were measured before and after the roasting process. We determined the residual rate after the roasting process. γ-BHC was not detectable at all, and more than 90% of chlordane was lost after the roasting (3.1 and 5.1% of chlordane remained in the beans spiked with 0.2 and 1.0 μg/g of chlordane, respectively). A low level of heptachlor (0.72%) was left in the coffee beans spiked with 1 μg/g of heptachlor. Disappearance of γ-BHC during the roasting process may be due to the high vapor pressure of γ-BHC, while chlordane has a lower vapor pressure. We also examined the behavior of piperonyl butoxide and atrazine during the roasting process. Piperonyl butoxide behaved similarly to chlordane, but atrazine disappeared after the roasting process, because it is unstable to heat.