The article presents a paleopathological analysis of two cranial samples from pre-Columbian Cuba: the Siboney (also known as Archaic) sample consisting of 40 individuals and the Taíno sample composed of 27 individuals. The Siboney are believed to have arrived to Cuba around 5000 years ago, and the Taíno inhabited the island since approximately 500 AD until decimation by the newcomers from the Old World. All the Taíno crania exhibit fronto-occipital artificial deformation. The main focus of the study is oral pathologies and bone abnormalities observed in the samples and how these reflect the differences between the two groups and individuals within each of them. Dental pathologies (caries, abscesses, antemortem tooth loss, and dental calculus) are more frequent in each sample's male and elder groups. The two samples compared together are close in the frequencies of caries, abscesses, and AMTL, while dental calculus is more frequent among the Taíno. The two cultural groups had different subsistence strategies: the Siboney were hunter-fisher-gatherers with the exception of the Canímar Abajo subgroup, for whom consumption of cultigens is proved, the Taíno were agriculturalists. In paleopathological studies, agricultural subsistence is usually associated with a higher rate of caries and lower rate of dental calculus. However, even after excluding individuals from Canímar Abajo from the Siboney sample, the difference in the caries rate between the two samples stayed insignificant. This could be due to carbohydrate-rich fruits that played an important role in the Archaic population’s diet. Pathological markers observed in the studied crania were classified according to Donald Ortner’s typology of bone abnormalities, which includes four major categories (abnormal bone size, abnormal bone or bone group shape, abnormal bone formation and abnormal bone destruction) and subcategories within them. Such an approach focuses mainly on the appearance of the lesions rather than on their possible causes. Pathological markers seen in the samples can suggest infectious, neoplastic, mycotic diseases, metabolic disorders. Possible antemortem traumas are infrequent in both samples. Specific to the Taíno crania is premature suture closure, which most probably is the consequence of artificial cranial deformation. In general, the analysis did not reveal significant differences in the two group's pathological statuses.