Citrus is the highest-value fruit crop in terms of international trade. However, citrus species are susceptible to several diseases caused by different types of micro-organisms which directly cause a decrease in production leading to economic losses. Since the last half-century, citrus industry in Uruguay has a strong socio-economic impact and is constantly evolving to stay competitive, including strategies as the incorporation of new varieties and high yielding orchards. Nevertheless, despite the existence since 2010 of the National Citrus Sanitary and Certification Program, none or very little information about the sanitary status of these citrus plantings regarding viruses and viroids was available. The incidence of citrus tristeza virus (CTV), citrus psorosis virus (CPsV), satsuma dwarf virus (SDV), citrus exocortis viroid (CEVd), hop stunt viroid (HSVd), citrus dwarfing viroid (CDVd), citrus bark cracking viroid (CBCVd) and citrus bent leaf viroid (CBLVd) was established, as well as CTV genotypes circulating in the country. Using molecular biology methods, 1175 samples from Valencia and Navel sweet oranges, Afourer and Clementine mandarins, and lemons, randomly collected from seven citrus-producing departments were analysed. Only 6% of the sampled citrus plants were pathogen-free, while 93% of them were CTV positive. SDV, CBLVd and CBCVd were not detected. Co-infections were very frequent finding plants with as many as four pathogens at the same time, being CTV present in all co-infected plants. This is the first comprehensive sanitary report of several citrus-infecting viruses and viroids in Uruguayan citrus groves, as well as the main CTV circulating genotypes in the country.