Shallot (Allium cepa var. ascalonicum) is one of the important vegetable commodity. The problems encountered in the cultivation of shallot is the disease caused by a virus which can reduce the quality and yield quantity. This study aimed to determine the group of viruses that infect shallot and geographycal distribution in Brebes and Cirebon Districts. The activities carried out by plant sampling in September 2013 (dry season) and April 2014 (rainy season). Identification of virus carried in the Virology Laboratory of Indonesian Vegetables Research Institute to perform testing using RT-PCR. The results showed that: (1) the high incidence of viral symptoms depend on cropping patterns, use of improved varieties, plant age, environmental conditions around the plant, (2) generally famers in Brebes and Cirebon Districts planted Bima Curut varieties, (3) geographycal distribution Potyvirus group, Allexivirus, and Carlavirus quite extensive in Brebes and Cirebon regions, (4) detected viruses from samples of Brebes District : Potyvirus group 92.30%, Allexivirus 92.50%, and Carlavirus 99%, and (5) detected viruses from samples of Cirebon District : Potyvirus group 96.43%, Allexivirus 96.15%, and Carlavirus 93%. The implications of the infection of the above three groups of viruses on the plant can decrease the production of shallots 21.57–51.90%.