ABSTRACT Stump removal is considered as the most effective method to reduce losses caused by root rot fungi, including Heterobasidion root rot. To evaluate the persistence of Heterobasidion spp. in root fragments left on site after stump removal, and to analyse the ecological impact of stump removal, five permanent sample plots were established in Latvia and samples were taken immediately after stump removal and 6 years later. In total, 1008 roots of 200 Picea abies stumps were measured and sampled immediately after stump removal. In total, Heterobasidion was detected in 0.7% of healthy looking roots, 2.0% of discoloured roots and 21.4% of decayed roots. Six years later, a total of 203 root fragments were collected in stump removal areas, and Heterobasidion was isolated from 1.5% of the collected root pieces. Fungal diversity was higher in root fragments collected in sample plots 6 years after stump removal compared with fungal diversity in roots immediately after stump extraction, and the species were significantly different. In conclusion, stump removal could be used in areas heavily infected by root rot fungi, and this method will likely not have a negative effect on the total amount of saproxylic fungi.