Root rot caused by Heterobasidion poses a severe threat to sustainable forestry in managed Scots pine stands in Sweden. In Scots pine, the disease remains hidden in the roots, leading to tree mortality and growth losses. Its cryptic nature often results in underestimated losses and insufficient management action. This thesis aims to highlight the issues posed by Heterobasidion in typical forest conditions, explores more efficient methods for disease identification, and assess the potential for future breeding of resistance in Scots pine. This work has been conducted under a combination of field and greenhouse conditions. Scots pine trees in stands designated as low-risk sites for Heterobasidion infection were examined for signs of infection in the crown. Subsequently, trees were uprooted, and samples were analysed for the presence of Heterobasidion infection. Drone imagery was used, and bud samples were retrieved for genetic analyses. In the greenhouse, the histological response to infection was analysed. A key finding of this study was the high prevalence of hidden infections in the roots of Scots pine trees on low-risk sites. Furthermore, the prevalence of these infections was positively correlated with site index, meaning that trees on higher-fertility soils were more likely to be infected. This finding calls for a change in forest management practices, specifically the application of stump treatment to Scots pine wherever Heterobasidion annosum is present in Sweden. Scots pine's response to infection, characterized by the formation of traumatic resin ducts, is local and impractical for effective disease detection or dating of infections. The use of drones equipped with RGB sensors demonstrated promising results, warranting further interest and development. Research is needed to explore how this technology can be applied to identifying Heterobasidion among other stressors. Heterobasidion is clearly a significant issue in Swedish forestry that deserves more attention. This thesis establishes that a promising genetic component can aid in selecting more resistant trees. In summary, this thesis underscores the cryptic nature of Heterobasidion disease on Scots pine, introduces available tools, and highlights the promising potential for further development.