Javamide-I/-II are anti-inflammatory compounds found in coffee beans. However, potential effects of roasting on javamide-I/-II in coffee beans are currently unknown. Therefore, in this paper, the effects of roasting on javamide-I/-II were investigated in Arabica and Robusta beans. Coffee beans were roasted light, medium and dark, and the amounts of javamide-I/-II in the beans were quantified by a HPLC method. The data showed the different amounts of javamide-I/-II in the beans; not detected and ≤ 3.1 mg in Arabica beans, and 0.5-3.7 mg and 1.0-13.8 mg in Robusta beans, respectively. Furthermore, the data showed that roasting process significantly reduced the amounts of javamide-I/-II in both Arabica and Robusta beans (p < 0.05). These data were also confirmed by multivariate analyses. Additionally, these differences were validated in light, medium and dark roast coffee products in the market. Altogether, roasting can have a significant impact on javamide-I/-II amounts in coffee beans.