Leprosis, caused by citrus leprosis virus (CiLV) and transmitted by the tenuipalpid mite Brevipalpus phoenicis, is one of the most important viruses of citrus in the Americas. Sweet oranges (Citrus sinensis L. Osb.) are highly susceptible to CiLV, while mandarins (C. reticulata Blanco) and some of their hybrids have higher tolerance or resistance to this disease. The mechanisms involved in the resistance and its inheritance are still largely unknown. To study the quantitative trait loci (QTL; quantitative trait loci) associated with the resistance to CiLV, progeny analyses were established with 143 hybrid individuals of ‘Pêra’ sweet orange (C. sinensis L. Osb.) and ‘Murcott’ tangor (C. reticulata Blanco × C. sinensis L. Osb.) from controlled crossings. Disease assessment of the hybrid individuals was conducted by infesting the plants with viruliferous mites in the field. The experiment consisted of a randomized completely block design with ten replicates. The evaluated phenotypic traits were incidence and severity of the disease on leaves and branches, for a period of 3 years. The MapQTL™ v.4.0 software was used for the identification and location of possible QTL associated with resistance to CiLV on a genetic map obtained from 260 AFLP and 5 RAPD markers. Only consistent QTLs from different phenotypic traits and years of evaluation, with the critical LOD scores to determine the presence or absence of each QTL calculated through the random permutation test, were considered. A QTL was observed and had a significant effect on the phenotypic variation, ranging from 79.4 to 84% depending on which trait (incidence or severity) was assessed. This suggests that few genes are involved in the genetic resistance of citrus to CiLV.