In 2006, Freire won his second consecutive Brabantse Pijl. His stage 3 win at Tirreno–Adriatico allowed him to lead for two days. At the Tour de Suisse, he survived an early break of four riders to win alone on stage 7. Freire won the fifth and ninth stages in the 2006 Tour de France and was contesting the points classification when he retired due to illness. During stage twelve, he was in a breakaway with three others. Freire's career has been blighted with injury and lay-offs. He had back problems, saddle sores and neck problems.