The submarine environment is unique in that there is limited space and no sunlight, which may negatively affect skeletal health and lead to accelerated bone loss, osteoporosis, and fractures. BACKGROUND The primary purpose of this study was to determine whether there was an association with submarine service, specifically time spent at sea, and bone mineral content (BMC) and bone mineral density (BMD) of the lumbar spine and dual proximal femur (total hip and femoral neck) measured by DXA. METHODS This is a cross-sectional study of 462 submariners 20-91 years old. Variables included in the analysis were age, height, race, alcohol intake, tobacco use, fracture history, conditions, and medications known to cause bone loss and osteoporosis and submarine service. RESULTS Of the submarine service predictors, only serving onboard a diesel submarine was determined to be independently associated with a reduction in BMD of the total hip and femur neck, while no submarine service predictor increased the odds of having low BMD. In submariners 50+ years old, the age-adjusted prevalence of osteopenia was 15.7 % (lumbar spine) and 40.4 % (femur neck), while the prevalence of osteoporosis was 4.8 % (lumbar spine) and 4.2 % (femur neck), rates that did not differ from NHANES 2005-2008. In submariners <50 years old, 3.1 % was below the expected range for age. The proportion of submariners 50+ years old that met the FRAX criteria for pharmacological treatment was 12 %. CONCLUSIONS Intermittent periods of submergence that can range from a few days to 3+ months do not appear to compromise skeletal health differently than the general population.