Public health recommendations do not distinguish between vitamin D2 and vitamin D3, yet disagreement exists on whether these two forms should be considered equivalent. The objective of the present study was to evaluate the effect of a daily physiological dose of vitamin D2 or vitamin D3 on 25-hydroxyvitamin D (25(OH)D) status over the winter months in healthy adults living in Dunedin, New Zealand (latitude 46°S). Participants aged 18–50 years were randomly assigned to 25 μg (1000 IU) vitamin D3 (n 32), 25 μg (1000 IU) vitamin D2 (n 31) or placebo (n 32) daily for 25 weeks beginning at the end of summer. A per-protocol approach, which included ≥ 90 % supplement compliance, was used for all analyses. Serum 25-hydroxyvitamin D3 (25(OH)D3), 25-hydroxyvitamin D2 (25(OH)D2) and parathyroid hormone (PTH) were measured at baseline and at 4, 8, 13 and 25 weeks. Geometric mean total serum 25(OH)D concentrations (sum of 25(OH)D2 and 25(OH)D3) at baseline was 80 nmol/l. After 25 weeks, participants randomised to D2 and placebo had a significant reduction in serum 25(OH)D3 concentrations over the winter months compared with vitamin D3-supplemented participants (both P< 0·001). Supplementation with vitamin D2 increased serum 25(OH)D2 but produced a 9 (95 % CI 1, 17) nmol/l greater decline in the 25(OH)D3 metabolite compared with placebo (P< 0·036). Overall, total serum 25(OH)D concentrations were 21 (95 % CI 14, 30) nmol/l lower in participants receiving vitamin D2 compared with those receiving D3 (P< 0·001), among whom total serum 25(OH)D concentrations remained unchanged. No intervention-related changes in PTH were observed. Daily supplementation of vitamin D3 was more effective than D2; however, the functional consequence of the differing metabolic response warrants further investigation.