Can Vitamin D3 cause kidney stones?

Supplementing with too much vitamin D (with calcium) has the potential to increase serum calcium levels and increase the risk of kidney stones in some individuals. A blood test that measures the vitamin D metabolite 25(OH)D can help determine whether your intake of vitamin D safely meets your individual nutritional needs. Continue working with your physician for individual guidance, and consider asking about regular blood tests to monitor your serum 25(OH)D level.

High doses of Vitamin D can be associated with calcium deposits, but this is usually only seen in extremely higher doses of Vitamin D (in the range of 50,000-100,000 iu daily). More than likely your kidney stones and vitamin D intake are not connected. 

The dose of Vitamin D being used should be adjusted based on a blood Vitamin D test to see where an individual's levels are at. It's possible that your Naturopath is wanting to correct a Vitamin D deficiency or using this higher dose as part of your treatment with Fibromyalgia, since lower vitamin D status is associated with higher anxiety and depression with those diagnosed with Fibromyalgia (1). 
It's best to communicate with your naturopath to fully understand the recommendations given and help you be active in the treatment process. Typical daily needs for Vitamin D in adults range from 500-1000 iu daily depending on age and climate. 
1. Armstrong, D. J., et al. "Vitamin D deficiency is associated with anxiety and depression in fibromyalgia." Clinical rheumatology 26.4 (2007): 551-554.

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