We use the temperature dependent c axis critical current and characteristic gap voltage as temperature gauges to assess the self-heating in stacks of intrinsic Josephson junctions etched out from the ultrathin Bi2Sr2CaCu2O8+δ (BSCCO) single crystals. The thermal resistance which characterizes the overall cooling efficiency is found to be ∼120–160 K mW−1 for the two stacks studied. This value is in agreement with earlier reports for stacks of similar geometry, while it is about two to three times higher than for simple mesas made on the surfaces of mm-size BSCCO single crystals. The suggested method can guarantee the validity of the temperature estimations inside the stacks of various geometries and different cooling efficiencies without the need for attaching additional thermometers.