Hypovitaminosis D is a prevalent micronutrient deficiency that can be severe and hard to treat in children with short bowel syndrome, a condition treated with substantial bowel resection. Surgically altered bowel anatomy then results in iatrogenic digestion and absorption limitations that require short- and long-term management and follow-up. Care of children with hypovitaminosis D standardly includes prescription dietary micronutrient supplementation, sometimes in irregularly high doses. This commentary responds to a pediatric case of vitamin D toxicity and suggests micronutrient-prescribing risk mitigation strategies in light of the absence of regulatory oversight of over-the-counter dietary supplements, inadequate insurance coverage, and easily available commercial retail products.