Spanish doctor Eufemiano Fuentes, the central figure in the trial that followed a probe into a doping ring in cycling, was given a one-year prison term last month for endangering public health.
The judge ordered the destruction of evidence including bags of blood possibly belonging to athletes from sports other than cycling.
The decision disappointed sports and anti-doping bodies, denting hopes that the case would unmask other athletes involved in illegal doping, and prompted widespread condemnation.
"The UCI can confirm that it will appeal the decision...not to release to the UCI and other anti-doping organizations the more than 200 bags of blood and other evidence gathered in police raids in 2006, which were presented in the trial of Spanish doctor Eufemiano Fuentes," the UCI said in a statement.
The Spanish Anti-Doping organisation (AEA) has already decided to appeal against the decision, while the World Anti-Doping Agency (WADA) has until May 17 to make a decision.
Fuentes, who protested his innocence, said in his opening testimony that he had clients in sports including soccer, tennis, athletics and boxing.
(Writing by Gregory Blachier; Editing by Clare Fallon)