Baptiste chose athletics over football when a ligament injury whilst only 14 ruled him out of the sport. Speaking of the injury Baptiste said "My main passion was football, but I saw the talent I had in athletics. I was playing for a Sunday League team in the Enfield area and I tore ligaments in my knee during a game. I was 14 at the time...I carried on playing and made it worse. I still can’t kick a football. Amazingly, the injury does not affect my running. When I kick a ball, my knee goes out of place, but when I run, it is fine." As a result of the injury Baptiste focused his attention on sprint running and he won the gold medal in the 100 metres at the European Junior Championships in Finland when only 18. He also anchored the 4x100 metres relay team to win his second gold of the competition. As a result, he was named junior male athlete of the year by the British Athletics Writers' Association. At the annual UK AAA Junior championships Baptiste won the 200 m title for three years in a row in 2002, 2003 and 2004 and the 100 m title twice in 2003 and 2004.