Populations of the Siberian flying squirrel Pteromys volans are declining as a result of insensitive forestry that has removed cavity trees. To conserve the cavities preferred by squirrels, we investigated the characteristics of the cavities they used as nests. We located 100 cavities with >3.0 cm entrance size (which they are able to enter), and investigated their use by the squirrels. We also recorded the entrance heights and entrance sizes of the cavities and the health and heights of cavity trees. The squirrels used 29 of 100 cavities. Entrance size and tree health strongly influenced cavity use, and entrance height had a weaker influence. Tree height was not correlated with cavity use. Squirrels preferred higher cavities with smaller entrances and on live trees. The entrance size of the cavities used was limited to ≤5.0 cm. Squirrels used 38% of live trees but only 14% of dead trees. In addition, the squirrels avoided cavities at low heights. They never used cavities <1.0 m above the ground. Therefore, cavities at >1.0 m height and with entrance sizes of 3.0 to ≤5.0 cm on live trees were preferred. We suggest that cavities with these characteristics should be conserved to protect the habitats of Siberian flying squirrels.