A total of 2257 recently felled stumps were sampled from 22 mixed naturally regenerated forest stands in the Aosta Valley, western Italian Alps, and examined for Heterobasidion annosum butt rots. Disease incidence ranged from 6% to 71% depending on sites, and H. annosum accounted for 92% of the total number of diseased stumps. H. annosum incidence was significantly higher (Chi-squared multiple comparison tests, p < 0.05) on Norway spruce (44%) than on the other tree species (silver fir = 18%, larch = 12% and Scots pine = 6%). Based on the information on the airborne inoculum composition of the fungus, all the three European species of H. annosum were present, with a variable frequency, depending on site. A partial least squares regression analysis showed that the relative abundance of Norway spruce and four variables describing the size of trees were the best predictors for the incidence of H. annosum butt rots. A model having these variables as predictors was developed (r2 = 0.75; p < 0.001) and successfully validated on five additional forest stands. An estimate of the losses in yield and value of timber associated with the disease, i.e. direct losses, was also carried out in the forests included in the survey. The percentage of direct financial losses was either comparable or lower than the average level of disease incidence.