We have studied the decay kinetics of two-dimensional holes on SrTiO₃(001) surfaces using scanning tunneling microscopy(STM). We have created nanoscale unit-cell-deep holes on (001) terraces using a STM nanofabrication technique, and have performed real-time observation of the decay of the holes in a temperature rage of 700 ∼ 800°C. From the observed time dependence of hole areas during decay, we have found that the rate limiting process of the decay is the surface diffusion. We have also investigated the effect of the existence of substrate steps and islands on the hole decay. [DOI: 10.1380/ejssnt.2006.307]