Founded in 1993 through the collaboration of scholars and artist, the Museum was inaugurated under the aegis of the Armand Hammer Center for Leonardo Studies of the University of California at Los Angeles. Conceived as a transposition, both concrete and virtual, of the "Imaginary Museum", it was officially recognised as a Museum of Public Interest in 1999.

It is the first museum to attempt to trace the complex personality of Leonardo in each of its manifold aspects and fields of interest. His activity as artist, scientist, inventor and designer is illustrated with continuous reference to his biography and the places frequented by him. This voyage through the mind and the oeuvre of Leonardo has been made possible by an exhibition that includes all of the reproductions of his pictorial masterpieces, facsimiles of his manuscripts and even a sampling of Leonardo's fingerprints. Unique of its kind is the "Leonardism Archive", the largest existing collection of examples and documentation of the use and abuse of Leonardo's image, from art to the mass media.

The collection also contains originals, including some paintings by members of Leonardo's circle, among the Madonna delle Minime, the Magdalene, the Young Christ at the Age of Twelve, and rare instruments in use in Tuscany in Leonardo's day, such as the "Ritrecine of Leonardo" [horizontal waterwheel]. Bearing witness to Leonardo's fame among his contemporaries are some rare engravings, among them two "Knots" dating from 1505-1507 engraved by Dürer to a design of Leonardo. The display is completed by over 60 models skillfully reconstructed on the basis of his projects, some of them really functioning, such as clocks, fountains, the "painter's house", the theatre of the "Mountain that opens" and other wonders of "Leonardism", including memorabilia and two autograph works by Duchamp.

Recently rearranged, the museum occupies the underground Gallery and the Ancient Wine Cellar of the Castle of the Guidi Counts, whose entrance is at Via Montalbano 2.

Now in the implementation stage is the project "Garden of Leonardo and of Utopia", planned as an outdoor section of the Museum situated in Via Collinare, a few hundred meters from the historic centre of Vinci.