Baptist Medical Center Downtown, a 599-bed tertiary hospital, is the flagship of Baptist Health in Jacksonville, Florida. The hospital is centrally located on the south bank of the St. Johns River, serving a region that is expanding both geographically and economically.

Baptist Downtown provides a comprehensive range of services, including: cardiology and cardiovascular care through Baptist Heart Hospital; oncology (including gynecologic oncology); women's health services, including obstetrics, gynecology and a Women's Health Center; and ophthalmology. Other major services include: emergency care (including Life Flight's air ambulance, the adult emergency center, the children's emergency center and hyperbaric medicine), critical care, bloodless medicine and surgery, pulmonary services, a sleep disorders center, pastoral care, radiology, rehabilitation, and psychiatry/psychology. Additionally, Baptist Downtown has the following regional referral centers: Jacksonville Orthopedic Institute, located in the Reid Medical Building; and Baptist Cancer Institute, located in the Edna Williams Cancer Center. The downtown campus is home to Wolfson Children's Hospital, the area's only children's hospital; and adjacent to the downtown campus is Nemours Children's Clinic a premier, pediatric research clinic.

Baptist Health incorporates the tertiary hospital in downtown Jacksonville, a 122-bed full service medical center in Jacksonville Beach, a 54-bed acute care hospital in Amelia Island and a brand new full service hospital in South Jacksonville.