Most studies on spatial memory refer to the horizontal plane, leaving an open question as to whether findings generalize to vertical spaces where gravity and the visual upright of our surrounding space are salient orientation cues. In three experiments, we examined which reference frame is used to organize memory for vertical locations: the one based on the body vertical, the visual-room vertical, or the direction of gravity. Participants judged interobject spatial relationships learned from a vertical layout in a virtual room. During learning and testing, we varied the orientation of the participant's body (upright vs. lying sideways) and the visually presented room relative to gravity (e.g., rotated by 90° along the frontal plane). Across all experiments, participants made quicker or more accurate judgments when the room was oriented in the same way as during learning with respect to their body, irrespective of their orientations relative to gravity. This suggests that participants employed an egocentric body-based reference frame for representing vertical object locations. Our study also revealed an effect of body-gravity alignment during testing. Participants recalled spatial relations more accurately when upright, regardless of the body and visual-room orientation during learning. This finding is consistent with a hypothesis of selection conflict between different reference frames. Overall, our results suggest that a body-based reference frame is preferred over salient allocentric reference frames in memory for vertical locations perceived from a single view. Further, memory of vertical space seems to be tuned to work best in the default upright body orientation.