Root rots are considered the most important forest diseases in Estonia, causing serious concern in forest management. The majority of trees infected by forest pathogens lack easily-detectable visual symptoms, making it difficult to detect decay in a tree. We assessed the general health condition of visually healthy trees in intensively managed Norway spruce (Picea abies L. Karst.) and Scots pine (Pinus sylvestris L.) stands with resistography in order to identify trees infected by root rot. We found that 8.0% of Norway spruces and 1.6% of Scots pines had well-developed internal decay on the root collar regardless of having no external symptoms of root rot. Visually healthy trees growing on permanent forest land experienced more decay than trees growing on former agricultural land. The radial proportion of decay of damaged trees was 61% in Norway spruces and 35% in Scots pines. The results suggest that resistography can be used as a reliable method for tree vitality assessment.