Climatically-driven surface temperature fluctuations disturb the steady state geotherm, and affect vertical heat flow measurements in shallow (<1000 m deep) boreholes. We investigated the causes of variability in reconstructed paleotemperature recorded by boreholes with a well constrained regional dataset from Tasmania, and a global synthesis. Variability between reconstructed past temperature changes is lower at local rather than regional scales. Climatic factors influence the magnitude of variability between boreholes, with non-climatic factors including topography, lithology and land use representing secondary measurable influences. The magnitude of variability means that paleotemperature corrections for heat flow will generally increase the accuracy, but not the precision of heat flow measurements.