Coffee (Coffea arabica L.) is one of the most important cash crops in Ethiopia. Coffee Berry Disease (CBD) caused by Colletotrichum kahawae is the severe disease threatening coffee production in most coffee-growing regions of the country. Field survey was conducted in three major coffee growing districts (Abaya, Bule Hora and Kercha) of Borena and Guji zones during 2012 cropping season to determine the incidence, severity and prevalence of CBD. CBD was prevalent in all the surveyed districts with the overall mean incidence and severity of 49.3 and 14.7%, respectively. Laboratory experiment was conducted at Haramaya University to investigate the characteristics of C. kahawae and other fungal pathogens associated with coffee berries. The proportion frequencies of infected and non-infected coffee berries were ranged from 24-42 and 3-21%, respectively. C. kahawae, F. lateritium and Phoma spp. of fungal pathogens were isolated from infected coffee berries with the proportions of 89.2, 15.2 and 3%, respectively. In general, the study revealed high occurrence, distribution and contamination of CBD in the study areas. Therefore, more extensive empirical assessment of the amount of yield loss due to CBD on most grown varieties in the areas and developing or introducing resistant varieties need to have high priority for developing management options which may enhance sustainable coffee production in the country.