The Serie A powerhouse have moved to publish a statement on their official website to make it clear they are not involved in the Operacion Puerto scandal
A Spanish paper published a document allegedly being used as evidence in the case that appeared to link Milan with Fuentes, but the club have stressed they have never had any contact with him.
"AC Milan have never had direct or indirect contact of any nature with Dr Eufemiano Fuentes," the statement reads.
"Any references to the activities of doctor Fuentes in relation to Milan are the result of false interpretations or a mistake.
"Milan reserve the right to take legal action against anyone who claims, suggests or insinuates something contradictory."
Fuentes, the doctor at the centre of the Operacion Puerto doping case, recently admitted to having worked with footballers as well as cyclists and athletes, but has so far refused to disclose the names of those involved.
Operacion Puerto investigated allegations of doping in sport and the suspected supply of several high-profile cyclists with EPO and other performance-enhancing drugs.
Police working on the operation arrested Fuentes in 2006 and seized 200 blood bags from his premises. He is currently on trial in Spain charged with breaking public health laws.