Based on seven G. arborea clonal trials, established in south Pacific of Costa Rica, it was determined the genetic control of tolerance in stem-rot, based on a collection of genotypes selected as plus trees in northern and southern regions in the country. The trials were established following GENFORES genetic design, which consisted in a complete randomized block design with six blocks and, each parcel conformed by three pairs of ramets, randomly assigned within blocks. Trials were evaluated based on severity methodology for stem-rot disease, which is based on five categories, where the first is assigned to completely healthy trees and, the fifth to those trees completely dead and rot. Other traits were also evaluated, like DBH, total height and sociological position. SELEGEN software (EMBRAPA, Brazil) was utilized to obtain all genetic parameters. In each clonal test was established a ranking for genetic tolerance to disease. Clones were assigned to three group categories: low, medium and high genetic tolerance. Mean clonal heritabilities (h(2)mc) ranged from 0.45 to 0.63, meanwhile genetic variation coefficients varied from 7 to 18% in severity degree analysis and, from 25 to 50% in incidence analysis. Genetic correlations were highly significant and inversely proportional (r < -0.55) between sociological position and total height with severity and incidence of disease. It suggests that the taller the tree the less affected by the disease. Meanwhile, DBH was not correlated and independent to the presence of this disease. Clones 4, 24 and 25 from south provenance, and clones 4, 5 and 11 from northern provenance, were identified as the most tolerant to rot-stem disease and more secure to be utilized in commercial reforestation in the southern region of the country. Results were consistent and reveal a strong genetic control of tolerance to rot-stem disease.