Accurate estimates of population size and distribution are a prerequisite for effective management of populations, but for most species a reliable estimation of the absolute population size is very difficult. In 1998, the Finnish Ministry of Environment set up a working group to plan a national-level survey for estimation and monitoring of the population size of Siberian flying squirrel (Pteromys volans). In 2006, the population size was reported to be 143 000 females. However, evaluation of the magnitude of possible biases was not attempted. Our aim was to test the population size estimate by conducting a resampling study with the methods of the national survey on an eartagged population of flying squirrels. We found that the methods used in the national survey provide greatly upward biased estimates. Moreover, the magnitude of the bias in the method seems to be sensitive to the true population sizes rendering the method unsuitable for population trend monitoring purposes. Therefore, we caution against using the national survey method in monitoring or in making conclusions about the population size of the Siberian flying squirrel.