Vitamin D deficiency is endemic in people living in the Gulf states. We performed a retrospective analysis of data gathered at the first attendance of 82,396 Emirati nationals to outpatient diabetes, endocrinology and general primary care services at two centres in the United Arab Emirates during 2012-2016. Our aim was to explore associations between vitamin D status and markers of cardiovascular and bone health. In the study population, 67.1% of men and 73.5% of women had serum 25(OH)D of less than 50 nmol/L, with the lowest levels being found in young adults. Among Emirati adults with type 2 diabetes, serum 25(OH)D < 50 nmol/L was associated with an increased risk of a coexisting adverse total cholesterol:HDL (TC:HDL) ratio (odds ratio 2.13 (1.60-2.84), p < 0.001). Correcting for age, sex, body mass index, HbA1c and statin therapy, an increase in 25(OH)D of 1 nmol/L was associated with a 0.01 unit reduction in TC:HDL in this population. In a subset of 1064 adult individuals, 25(OH)D < 25 nmol/L was associated with a reduction in DEXA-measured z-score of -0.29 (-0.44 to -0.15, p < 0.001) at the femoral neck and of -0.25(-0.45 to -0.05, p = 0.015) at L1-4, corrected for body mass index, compared with individuals with 25(OH)D ≥ 75 nmol/L. Our findings raise concerns regarding lifetime burden of cardiovascular disease and bone health for young Emiratis with vitamin D deficiency.