San Juan ante Portam Latinam (Laguardia, Álava, Spain) is a small rock shelter located in the middle valley of the River Ebro, where a large number of individuals were buried at a time of transition from the Neolithic to the Chalcolithic (ca. 3000 cal bc). It is an outstanding archaeological site, due to the atypical choice of site for burials, large number of bodies, and numerous signs of violence observed. The population at the site comprises a minimum number of 338 individuals belonging to both sexes and all age groups. They display various kinds of pathologies, including at least 11 arrow wounds and four trepanations. The human remains are accompanied by a series of objects, such as lithic and bone implements, as well as personal objects of adornment. Among the few faunal remains found, a dog’s skull shows signs of decapitation. The site was sealed by the collapse of the rock overhang of the shelter, until it was discovered accidentally in 1985. A rescue excavation was carried out in that year, and this was followed up by two further excavations in 1990 and 1991. They were all directed by José Ignacio Vegas, under the sponsorship of the Diputación Foral de Álava.