Syphilis, together with its variant congenital syphilis, is a disease caused by Treponema pallidum subsp. pallidum. This paper documents possible new skeletal evidence for congenital syphilis from the Medieval Era (twelfth and thirteenth centuries CE) burial site of Medinaceli in the Province of Soria in North-Central Spain. What is involved is dental alteration due to congenital syphilis, mercury treatment, or a combination of both. This study focuses on the hypoplastic dental changes observed in a child approximately eight years of age. Only a fragmented skull with left maxilla and the left side of the mandible were preserved. Macroscopic analysis, X-rays, computerized tomography (CT) and mercury detection analysis by inductively coupled plasma mass spectrometry (ICP-MS) techniques were used to observe dental abnormalities. In addition to extensive caries in the upper second deciduous molar, pulpo-alveolar lesions and facial alterations were observed. The absence of the rest of the skeleton tends to make a diagnosis of congenital syphilis difficult. However, the dental stigmata observed do permit a reasonable diagnosis.