The study, published Monday in the Canadian Medical Association Journal, found that kids who drank only non-dairy milk were more than twice as likely as children who drank only cow's milk to be vitamin D-deficient.
Vitamin D, known as the sunshine vitamin, plays a critical role in bone development. Low levels of vitamin D can cause bone weakness and, in severe cases, rickets — a condition that causes bones to become soft and can potentially lead to skeletal deformities.
In Canada, cow's milk and margarine are required by law to be fortified with vitamin D, which is also found naturally in fish, liver and egg yolks. Most of the body's vitamin D stores arise from exposure to sunlight, which converts cholesterol in the skin to vitamin D3. But from late fall through to spring, there is not enough sunlight in Canada for the body to make vitamin D, so dietary sources are critical to maintain bones and to optimize health.
Based on a recommendation by the Institute of Medicine, the level of vitamin D in a child's blood should measure at least 50 nanomoles per litre to ensure good bone development.
"When we looked at what different kinds of milk and milk beverages children were drinking, we found a gradient in their vitamin D levels," said principal investigator Dr. Jonathon Maguire, a pediatrician and researcher at St. Michael's Hospital in Toronto.
"What we found was that in children who were drinking only non-cow's milk beverages, they had a lower level (of vitamin D). About five per cent who were only drinking cow's milk and about 11 per cent of children who were drinking only non-dairy milk were below that level (of 50 nmol/l)," he said.
"Among children who drank non-cow's milk, every additional cup of non-cow's milk was associated with a five per cent drop in vitamin D levels per month."
The study involved 2,831 healthy children aged one to six who were recruited from seven Toronto pediatric or family medicine practices that are part of a research network called TARGet Kids!
Researchers found that 87 per cent of children in the study predominantly drank cow's milk, while 13 per cent drank non-cow's milk.
There are a variety of reasons some parents give their kids non-dairy milk products, including lactose intolerance, allergies and a perception that they may be a healthier choice.
"I think there are perceived health benefits," said Maguire. "The question is: are there actual health benefits? And that's one of the reasons we did this study."
All cow's milk sold in Canada has to be fortified with 100 international units (IU) of vitamin D per cup, and the dairy products are carefully regulated with content testing.
But non-dairy milk beverages made from such plant-based products as soy, rice and almonds fall outside the legislation, he said.
"There doesn't have to be vitamin D in non-dairy milk. So some do contain it and some don't."
Maguire advises parents who choose non-dairy milk for their children to check the nutritional information box on the product to see whether it contains vitamin D and how much.
Labels on many of the commercial plant-based milk products say they are enriched with vitamin D in quantities similar to the amount required for cow's milk.
Sara Loveday, a spokeswoman for U.S.-based White Wave Foods, said by email that the company's Silk-brand almond, soy and coconut milks are fortified with vitamin D, "and our products are clearly labelled to indicate its presence."
Earth's Own Food, a B.C. company that produces So Good, So Nice and Almond Fresh soy and almond milks, also fully fortifies its products, said marketing director Brendan Kelly.
While the decision to enrich a non-dairy product is voluntary, Health Canada has guidelines for fortification that follow a specific schedule to make plant-based products "nutritionally adequate alternatives to milk," Kelly said from Vancouver.
Earth's Own soy and almond milks contain 45 per cent of the recommended daily intake (RDI) of vitamin D per 250 millilitres, the same amount contained in cow's milk.
"So it's intended that it mirror milk or the nutrients in milk," he said, noting that like cow's milk, soy also naturally contains protein, which the other plant-based products do not.
While some companies follow the guidelines to enrich their non-dairy beverages, Kelly conceded there are some producers in the industry that don't fortify their products with vitamin D.
Still, Maguire said it's important to make sure kids are getting enough of the nutrient.
"I think we need to be a little bit careful about (a product's) vitamin D content and pay particular attention to the back of the bottle," he said, adding that the information should ideally be put on the front label so it's easy for consumers to see.
"It's a little unclear to me at least why cow's milk is fortified with vitamin D universally, but these alternatives that some parents are choosing are not."
Follow @SherylUbelacker on Twitter.
Note to readers: This is a corrected version. A previous story erroneously reported that more than 3,800 children were in the study.Suggest a correction