On his second day on the stand, Fuentes, who denies involvement in doping, said he could identify to whom the blood in the numbered bags belonged, prompting a request by the Italian Olympic Committee, represented at the trial in Madrid, that he do so in court.
Judge Julia Santamaria said she would not prevent him from revealing the names but would not force him to do so, saying it would infringe the rights of those implicated.
Fuentes and four other defendants, including his sister Yolanda, are appearing in court almost seven years after anabolic steroids, transfusion equipment and blood bags were seized as part of a investigation code-named "Operation Puerto".
The closely-watched and much-delayed trial began on Monday and when Fuentes took the stand on Tuesday he told the judge he had clients in sports other than cycling, including football, tennis, athletics and boxing.
The proceedings have attracted international scrutiny because anti-doping authorities, who along with CONI and several sporting organisations are taking part in the trial, are hopeful it will finally lead to evidence of wrongdoing by athletes in other sports being made available.
A World Anti-Doping Agency request for access to the blood bags has been repeatedly denied by the Spanish authorities, and the body await the judge's ruling on their latest petition made this week.
Fuentes did reveal the name of one client on Wednesday, identifying former rider Jose Javier Gomez, now the president of Spain's association of professional cyclists and the director general of a government foundation that promotes sport for young people.
Fuentes also told the court he was aware that abnormally high levels of erythropoietin had been found in eight of the 92 blood bags seized in 2006 but said he had nothing to do with the presence of the artificial hormone.
"No product was ever added to the blood except legally established preservatives," Fuentes said.
"Such a small quantity (of EPO) can have no other explanation than that it was the remnants of a previous treatment."
Prohibited by anti-doping authorities since the early 1990s, EPO can help athletic performance by increasing the concentration of red cells and improving the amount of oxygen blood can carry to the body's muscles.
As Spain's current anti-doping legislation was not in force in 2006 when the police raids took place, Fuentes and his fellow accused are being tried for violating public health regulations and the prosecutor has asked for prison sentences of two years.
The blood bags were linked to more than 50 professional cyclists including German Jan Ullrich and Italian Ivan Basso, who were both excluded from the 2006 Tour de France.
Basso, a double Giro d'Italia champion, is due to give evidence next month along with Alberto Contador, the Spaniard stripped of one of his three Tour de France titles after testing positive for a banned substance.
Disgraced American rider Tyler Hamilton is also due to take the stand.
"I never put the health of the athletes at risk," Fuentes said.
"No athlete ever told me they had health problems and I was never the subject of a complaint."
On Tuesday, Fuentes refused to answer a host of detailed questions from lawyers representing organisations including WADA, the Spanish Cycling Federation and the International Cycling Union.
With Madrid competing with Istanbul and Tokyo for the right to host the 2020 Olympic Games, the Spanish government hopes the trial will help to dispel the impression that the Iberian nation has been soft on doping, particularly in cycling.
Due to end in mid-March, it will put cycling's problems with illegal drug use back in the spotlight after American cyclist Lance Armstrong this month admitted doping on each of his seven Tour de France victories.
- Politics & Government
- Italian Olympic Committee