Extra‐tropical cyclones are a relevant feature in the climate at middle and high latitudes. Despite their importance, most studies typically focus only on cyclones identified at a single atmospheric level and on events close to the surface. This paper provides a new perspective on the Southern Hemisphere (SH) cyclone events based on the multilevel cyclone tracking algorithm STACKER. The algorithm, using relative vorticity, detects the raw tracks at single levels and objectively combines them to provide the 3D events and their evolutionary timeline. As a result, a 3D cyclone climatology, based on ECMWF Reanalysis ERA‐I data from 12 pressure levels in the troposphere and lowermost stratosphere is presented. To the best of our knowledge, this is the first analysis carried out throughout the troposphere and the lowermost extratropical/subpolar stratosphere in order to give a comprehensive picture of the cyclone events as physical entities throughout their lifetime. Cyclone properties analysed are track densities, translational velocity, vorticity and lifetimes. For the subtropical and extra‐tropical SH, results support many previous ideas about cyclone characteristics, but new insights are also obtained. A total of 58,231 multilevel cyclone events lasting at least 2 days were detected, with vertical structures spanning two or more levels. This means an average of 303 cyclone events of all types per month, between 2001 and 2017, disregarding seasonality. Results show that cyclones are most frequently detected at the lowest levels of 925 and 700 hPa. By considering that cyclonic systems can be grouped into families according to their vertical extent, results per month on average show that shallow systems are the most frequent events with approximately 248 systems detected, followed by 43 intermediary and 11 deep events. Shallow and deep systems have a large percentage of events with genesis at 925 and 700 hPa. Density statistics show that shallow events are present at all latitude ranges mostly poleward of 30°S with high‐ and medium‐intensities, while intermediate ones are mostly restricted to mid‐latitudes and deep events are mostly confined to sub‐polar and polar latitudes. Cyclones over Antarctica seem to be mostly intermediary and deep cyclones, with longer lifetimes and lower velocities.