Health in archaeological populations needs to be investigated using a holistic approach. Molecular techniques, particularly multiplex PCR, can be used with paleopathology and dietary analysis to understand aspects of population health. This thesis demonstrates how spina bifida, a multi-factorial disease, can be investigated using this paleoepidemiological approach. Based on skeletal evidence, spina bifida was present in a pre-Columbian Cuban population from the archaeological site of Canimar Abajo. Molecular techniques were employed to examine disease potential, examining individuals for five single nucleotide polymorphisms associated with spina bifida. It is postulated that the combined effect of these polymorphisms, as well as dietary factors, determines the risk of the population for spina bifida, and that these factors came together to create the observed high disease prevalence. Therefore, this thesis demonstrates how the methods of molecular paleopathology, corroborated by dietary analyses, can be used within a paleoepidemiological framework to understand population health and disease.