Fuentes was once an athlete. He then became the team doctor of Team ONCE, Amaya and the Kelme. The former Kelme rider Jesús Manzano accused Fuentes of being involved doping. Fuentes retired as the team doctor of the Kelme team in 2005. At that time he had been the doctor of the Kelme team for 16 months. He announced that he was retiring from involvement with professional cycling citing health and family reasons as well as a desire to investigate retinoblastoma cancer in the Instituto del Cáncer de Canarias.
Fuentes was arrested by the Guardia Civil on May 22, 2006 together with the four others. The manager of the Liberty Seguros team Manolo Saiz, José Luis Merino a hematologist at an analytical laboratory in Madrid, Alberto León, a professional mountain biker and José Ignacio Labarta, who was at that time the assistant sports director of Comunidad Valenciana.
In Fuentes' clinic in Madrid, 100 blood bags were found which were suspected to belong to athletes that doped. The scandal that grew from the arrests implicated well-known road racing cyclists and include former Tour de France favorites Jan Ullrich, Ivan Basso, Francisco Mancebo, Michele Scarponi, José Enrique Gutierrez Cataluna, Roberto Heras, Alejandro Valverde, Dario Pieri and large parts of the Comunitat Valenciana and former Liberty Seguros cycling squads. Alberto Contador was also suspected as being involved with Fuentes. Fuentes continually denied having performed illegal operations and also said that he did not work exclusively with cyclists but had other athletes as clients such as footballers.