The present paper describes the study of a skeleton, kept at the Church of Santa Chiara in Urbino, Italy. Traditionally, this skeleton was thought to be that of the Duchess Eleonora Gonzaga della Rovere (1493-1550), but suspicion exists as to whether or not the remains might belong to another important personage of the Urbino Renaissance, Battista Sforza (1447-1472). Here, external observation of the skull and odontological examination of the mandible were conducted in an attempt to clarify the identity. Age estimates of the skeleton were found to be consistent with the age at death of Eleonora but not with that of Battista. Craniofacial superimposition using the portrait of Eleonora Gonzaga by Titian (Galleria degli Uffizi, Florence) shows that the face of Eleonora matches the skull fairly closely except for the length of the nose. The historical record and the age matching appear to provide strong evidence that the remains are those of Eleonora, and the discrepancies in the superimposition may suggest that the artist altered the dimension of the Duchess' nose, possibly to make the portrait correspond to his canons of classical beauty. The results highlight the potential of forensic methods as a key to understand the work of earlier painters.