With the aim of establishing the efficient placement of nest boxes to assist research, we investigated nest box selections by Siberian flying squirrels Pteromys volans. The influence of different factors on whether nest boxes were chosen by the squirrels, specifically tree type (broad-leaved/conifer), health of tree (dead/alive), size of tree in which they were installed, nest box height, and cavity and nest box density was examined in 10 small and windbreak forests sites from July 2010 to October 2011. Ninety-six nest boxes were observed 10 times each, 47 of which were used by the squirrels in the spring, summer and autumn. The results of model selection using a generalized linear mixed model showed nest box height and cavity density to be ranked most highly. Nest box height was positively correlated (coefficient = 3.57, SE = 0.80) with use by the squirrels. Cavity densities was negatively correlated (coefficient = -0.70, SE = 0.24) with the use. These results indicate that Siberian flying squirrels tend to select nest boxes installed in higher positions or in forests with a lower cavity density. Research into the squirrels thus can be made more efficient if a) nest boxes are installed as high as possible without interfering with research efficiency, b) in low cavity density forests, and c) by observing the boxes between spring and autumn.