The use of automated systems to record the identity of individual penguins and their movements in and out of a colony can provide an effective means of studying penguin biology remotely. A new gateway installed at the macaroni penguin colony at Fairy Point (513 breeding pairs in 2003) on Bird Island, South Georgia in February 2003 and the implantation of passive integrated transponders for identifying individuals is described. The reliability of the system in recording penguin arrival and departure during the end of the 2002/2003 breeding season and over the complete 2003/2004 breeding season was tested using an independent method of radio telemetry. Results from two seasons of trials indicated that there was only a 3.7% probability of the gateway missing a penguin in 2002/2003 (185 total logged crossings) and 3.9% in 2003/2004 (1,309 total logged crossings); this compared with probabilities of 16.2 and 7.9% using radio telemetry, both differences being highly significant. This automatic logging gateway is therefore shown to be a more reliable means of recording the transit of penguins between the colony and sea and, over the longer term, elucidating colony attendance and survival rates of this species at South Georgia.