Managing the availability of shelter sites is central to the conservation of vertebrate wildlife dependent on tree hollows (cavities) because hollow abundance has been reduced in many landscapes and trees do not typically acquire hollows until they are at least 100 years old. Artificial hollows (nest boxes) provide one option to offset local shortages in tree hollows. However, knowledge of preferred designs is required for this to be effective. We investigated nest box preference by the eastern pygmy-possum (Cercartetus nanus), a small marsupial recognised as threatened across part of its geographic range in eastern Australia. We installed nest boxes of four different designs in each of 30 plots where tree hollows were scarce. Designs showed no significant difference in thermal profile. We captured 223 adult and subadult pygmy-possums within 78% of the 120 boxes. Breeding females used boxes more frequently than adult males and showed a preference among the designs whereas males did not. Females favoured plywood nest boxes over a PVC design offering a horizontal cavity. Use of the PVC design increased when repositioned to present a vertical cavity. Thus, breeding females are selective of the cavities used to rear young, which may limit local population size.