The Dominican Church of the Holy Spirit of Vilnius, in Lithuania, overlies a number of subterranean chambers. Within these chambers are mummified and skeletonized human remains of both religious and laypeople, as well as wooden coffins and precious textiles most likely dating from the 18^th-19^th centuries AD. In 2011, at the request of the church officials, the Department of Anatomy, Histology, and Anthropology of the local university commenced an investigation enabling the documentation, study and conservation of this historic material with the study of 23 human mummies consisting of 15 adults, eight sub-adults and a number of isolated body parts. Following the external inspection, each body was carefully recorded and tissue and bone samples were obtained only from those subjects that displayed loss of substance, either determined by natural decay or other post-depositional changes. External observation and CT-scans of a subset of remains indicate a number of pathologies including arthritis, atherosclerosis, enamel hypoplasia, tuberculosis and pleural adhesions. The most interesting case was a female child mummy who revealed a combination of rickets and hydrocephalus. Palaeogenetic analysis of a subset of remains is ongoing to investigate bacterial and viral pathogens from within the collection.