The first thing i would advise you is to go to a pedodontist. There are special child toothpastes containing calcium and other ingredients that will help maintain the hygiene of your child's teeth. Though there are chances that the effect won't be shown up in milk teeth but it will help permanent teeth to grow without any problem
The cause of stains on milk teeth may be a developmental anomaly that took place when your child was still in foetus for e.g. mother encoutering a fever or any infection that affected teeth devemopment.
For more info on infant dentistry you can read the articles on our website....http://www.identalhub.com/articlecategory-children-dentistry-33.aspx
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