Sclerotinia sclerotiorum (Lib.) de Bary is a yield-limiting factor and the major disease of sunflower ( Helianthus annuus L.) in the temperate regions of the world. In this study we characterized resistance to S . sclerotiorum midstalk rot and morphological traits in a population derived from a cross between two Sclerotinia resistant lines. Phenotypic data for 114 F 3:4 lines and the two parents NDBLOS sel and K04 were obtained under artificial infection in field experiments which yielded moderate to high heritabilities. Our results suggest that S. sclerotiorum resistance is highly quantitative and that different genomic regions may mediate the resistance in different tissues of the plant. We found transgressive segregation for all three resistance traits suggesting that both resistant parents carried complementary QTL. In addition we investigated the segregation of two known QTL for midstalk resistance and found that one of them also acts as a major QTL in this cross between two resistant lines. Collectively our results suggest that a QTL stacking approach is a promising way to increase resistance to S. sclerotiorum in elite sunflower germplasm.