Inonotus obliquus, a well-known forest fungal pathogen, started gaining attention for its potential medicinal uses. Known as Chaga, the fungus has become prominent due to the bioactive compounds present in its conks. Forest owners are cultivating it to produce conks as a source of non-timber profit. However, not much is known about the natural occurrence of this pathogen, its formation of conks, the extent of decay in the infected trees, and the distribution of its basidiospores. Across 80 forest stands in Estonia dominated by Betula pendula, B. pubescens, Alnus incana, and A. glutinosa, the conks of I. obliquus were documented in 17 stands. The conks were more common in continental Estonia compared to the western islands. Among 800 randomly chosen trees, I. obliquus conks were documented on ten trees. Additionally, an asymptomatic I. obliquus infection was detected in one tree. After two years of spore trapping, I. obliquus basidiospores were detected only on four occasions, between the end of July and the beginning of September, and only at night. The proportion of rot damage in the total volume of model tree wood ranged from 8.6% to 58.5%. For fast and reliable detection of I. obliquus, TaqMan species-specific qPCR primers were developed and tested. •The rot damage caused by I. obliquus ranged from 8.6% to 58.5% of the host tree volume.•obliquus propagates its basidiospores only at night.•The basidiospores were released from the end of July to the beginning of September.•The conks of I. obliquus are equally likely to be found in Betula and Alnus stands.•1.25% of host trees were having I. obliquus conks.