During growing season of 2015-2017 (June-September), phytopathological surveys were conducted in the southern part of Azerbaijan. A total 263 suspicious tomato (Solanum lycopersicum L.) samples of various cultivars exhibiting symptoms of leaf curl, dwarfing, leaf narrowing, necrosis, mosaics or yellowing with reduced fruit yield and quality were collected in three regions (Jalilabad, Masally, Lankaran) of Azerbaijan. Collected samples were first tested serologically (rapid one-step assay AgriStrip, DAS-ELISA) depending on virus symptoms and then molecular tests (RT-PCR, PCR) were performed to confirm the virus presence. According to the result of serological tests, 179 samples (68%) positively reacted with the virus antibodies. DNA and RNA genome virus infections were confirmed by polymerase chain reaction (PCR) and reverse - polymerase chain reaction (RT-PCR). Results showed the presence of Tomato mosaic virus (ToMV), Tobacco mosaic virus (TMV), Tomato etech virus (TEV), Tomato spotted wilt virus (TSWV) and Cucumber mosaic virus (CMV) in tomato samples. CMV was the most common virus, infecting about 25% of the tomato samples. TMV and ToMV, infected tomato samples by about 21% and 13%, respectively, followed CMV in frequency. This study reports the natural incidence and prevalence of tomato viruses in the southern part of Azerbaijan.