Following a comprehensive restructuring of the Australian Paralympic Committee in 2002-03, the APC took total responsibility for the selection of athletes for Athens with board members acting as selectors. The APC established general and specific sport selection criteria with guidelines that required individual athletes to be ranked internationally in the top six, and teams to be ranked in the top five. Mainstreamed sports, through their National Sporting Organisations, and non-mainstream sports through advisory committees, recommended athletes and support staff for approval by the APC. The Australian Paralympic Team for Athens, comprised 151 athletes (91 men and 60 women) and 88 staff, was very lean – only half of the size of the Sydney 2000 contingent – as a result of the strict selection criteria and the absence of athletes with an intellectual disability.
Australia collected 101 medals in total, placing second overall and fifth on the gold-medal tally. The rising star was Matthew Cowdrey who was the youngest member of the Australian contingent at the tender age of 15. He won a total of seven medals (three gold, two silver, and two bronze), established two world and Paralympic records in the pool, and carried the Australian flag at the closing ceremony. Tim Sullivan continued a very impressive career, winning four gold medals on the track in athletics to add to five gold medals from Sydney. His Athens performance was recognized when he was named Paralympian of the Year in 2004. There were several other multiple medallists: swimmers Ben Austin, Chantel Wolfenden and Prue Watt all won six medals; track athlete Heath Francis won five medals; and cyclist Lindy Hou secured four medals. Six athletes won three medals each: Don Elgin, Neil Fuller, Kurt Fearnley and Darren Thrupp in athletics, and Kieran Modra and Christopher Scott in cycling.