The formation and annealing of individual amorphous zones in silicon have been studied using in situ transmission electron microscopy. This technique enables us to identify anomalous behavior that cannot be deduced from statistical studies. Zones were formed at room temperature by impacts of single 200 keV Xe+ ions and imaged using structure factor contrast under down-zone conditions. Irradiation to fluences in the range 1011–1012 ions/cm2, results in small zones of black contrast (typically of order 1 nm in radius) which are clearly visible with minimal overlap. In agreement with earlier work, we observe a reduction in the total volume of amorphous material upon annealing over a temperature range from room temperature to 500 °C. Disappearance of individual zones with the same starting radius is observed to occur over a wide range of temperatures and in a small number of cases, zones are observed to increase in size during annealing. A discussion of these effects, based on the bond defect or I–V pair is presented.