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Vitamin D - produced by the body after exposure to sunlight - is vital for good bone health.
The newly published study followed 126 women who gave birth at Dunedin's Queen Mary Maternity Centre between 2011 and 2013.
On average, rates of vitamin D deficiency were very high - 65% of mothers and 76% per cent of infants - and the rate increased in winter months to as high as 90% of infants.
There was evidence of rickets (weak or soft bones) in three infants.
``It is likely this data would reflect the Dunedin population as a whole,'' study co-author Ben Wheeler, of the University of Otago, said.
An earlier study had identified 60 children across New Zealand over a two-year period with rickets, Dr Wheeler said.
That study had targeted at-risk groups, so finding such a prevalence of vitamin D deficiency in women and babies who were previously considered low risk - let alone cases of rickets - was particularly surprising, he said.
``It's incredibly unusual, so it probably suggests how common mild degrees of rickets actually are.
``It is the most severe form of vitamin D deficiency, but it is probably a lot more common than we think.''
The Ministry of Health estimates around 5% of New Zealand adults are vitamin D deficient, and a further 27% are below the recommended blood level of vitamin D.
For the research, samples from the mothers and babies were taken from the first trimester until the end of exclusive breast feeding.
``We're seeing the cycle of vitamin D as it were, rather than taking one-off measures. Rates of deficiency are higher in winter and spring, but even in other months the rates are still relatively high,'' Dr Wheeler said.
Although the data was gathered in Dunedin, he suspected it reflected a wider, possibly national, problem.
``It's not just an isolated public health message for Dunedin - it's at the very least a South Island message.''
The issue was partly geographic - the South Island gets less sun than the North - but modern lifestyles, darker skin and covering up in clothing all increased the risk of vitamin D deficiency.
The same issues existed in the northern hemisphere, but because it was a known issue doctors promoted people taking supplements - a policy this new evidence suggested New Zealand should follow, Dr Wheeler said.
``At the very least the South needs to be added as an area where taking supplements is recommended.''
Current Ministry of Health advice is for doctors to only consider use of supplements.
``It's not even a recommendation, so it's very weak,'' Dr Wheeler said.
``A GP or a maternity provider in the South Island should be recommending for all women to be supplemented, and then women can make their own decisions ... as they do with all recommendations.''