Objective: Vitamin D deficiency is now recognised as a common health problem associated with various chronic diseases; however, it has not been fully elucidated among the minority groups. Here, we aimed to investigate the prevalence of vitamin D deficiency and its associated metabolic risk factors among North Korean refugees living in South Korea. Design: Cross-sectional analysis from the longitudinal cohort, the North Korean refugee health in South Korea (NORNS) study. Participants: A total of 386 North Korean refugees aged >= 30 years, who measured serum 25-hydroxy vitamin D (25(OH) D) level. Results: The prevalence of vitamin D deficiency (25(OH) D <20 ng/mL) was 87% and no participants had an adequate vitamin D level (25(OH) D >= 30 ng/mL). Underweight participants (body mass index (BMI) <18 kg/m(2)) had significantly lower 25(OH) D levels than individuals with normal BMI (>= 18.5 and <23 kg/m(2)). In the multivariate logistic regression analysis, the lowest 25(OH) D level (<10 ng/mL) was significantly associated with metabolic syndrome (OR, 6.37, 95% CI 1.34 to 30.3), high triglyceride (OR, 6.71, 95% CI 1.75 to 25.7), and low high-density lipoprotein (OR, 5.98, 95% CI 1.54 to 23.2) compared with 25(OH) D levels >= 20 ng/mL after adjusting for age, sex, season, length of residence in South Korea, physical activity and BMI. Conclusions: Vitamin D deficiency is very common among North Korean refugees in South Korea. Despite their lower BMI, vitamin D deficiency was associated with metabolic syndrome in this population.