Abstract: Coffee beans exposed to infection by microorganisms during storage, especially fungal infection which cause great damage to beans. This research aimed at studying the bad effect of fungal infection of stored coffee beans at the eastern zone of Saudi Arabia. Result showed that coffee beans contain number of fatty acids, namely caprilic, lauric, miristic, palmitic, palmitoleic, margaric, stearic, Oleic, linoleic, alpha-linoleic and arachidic acids. Treatment of beans with fungi led to increase in the percentage of miristic, margaric and stearic acids. With increasing the duration period of storage% of oleic acid of Harari verity showed its level before treatment at 0, 8, 25°C to be 42.28, 40.04 and 42.97%, respectively . These levels showed decreasing after storage for three months to be 37.24, 36.59 and 38.98% at the same degrees with increasing the period of storage. In the Barry, the level of the oleic acid recorded 42.36 and 41.77% at 8 and 25°C. These records decreased after storage to be 38.71%, 38.65% in the infected beans. These levels changed during storage at 0°C from 35.87% in the control, to 39.1% in the infected ones. Storage for 9 months at 25°C decreased the acid level to 25, 19.93% in both control and treated beans storage at 0, 8°C led to increase in acid level from 19.81, 19.36%, in control beans, to be 27.84, 19.74% in infected beans, respectively.