Embodiments are directed to establishing efficient virtual machine reference points and to specifying a virtual machine reference point to query incremental changes. In one scenario, a computer system accesses a stable virtual machine checkpoint that includes portions of underlying data stored in data storage, where the checkpoint is associated with a specific point in time. The computer system then queries the data storage to determine data storage identifiers that reference the point in time associated with the checkpoint and stores the determined data storage identifiers as a virtual machine reference point, where each subsequent change to the data storage results in an update to the data storage identifier, so that virtual machine reference point is usable to identify incremental changes from specific points in time on.