In a cross-sectional screening programme, we assessed serum vitamin D levels in adult Eritrean refugees recently arrived in Switzerland. Median vitamin D level among 107 participants (95 males and 12 females) was 27 nmol/l (interquartile range 23-42 nmol/l), 86% had insufficient vitamin D levels (≤50 nmol/l) and 36% severe deficiency (<25 nmol/l). In 29 participants who received single-dose intramuscular vitamin D substitution (300 000 IU), median vitamin D levels increased from 25 to 35 nmol/l after 3 months (p = 0.005); only 11 (38%) reached sufficient vitamin D levels. Eritrean migrants should be routinely screened for vitamin D deficiency. Single-dose intramuscular supplementation appeared to be insufficient to achieve optimal levels in the majority of participants.