Orthodontic treatment has been traditionally carried out with fixed appliances involving the use of stainless steel brackets and archwires. The challenge has been to move teeth and their roots effectively while minimizing iatrogenic damage such as root resorption and gingival inflammation. In recent years, with the development of new appliances and brackets such as self-ligating brackets and clear aligners there have been reports of improved periodontal status, less iatrogenic root damage and improved hygiene during treatment. Although these treatment modalities have been rapidly accepted in clinical practice, both clinical and basic science research data regarding their overall biological compatibility to support higher levels of evidence based dentistry (e.g, randomized clinical trials) is lacking. In other words, their advantages and disadvantages in this regard have not yet been scientifically evaluated. Such quantification will provide invaluable information for improvements in these treatment modalities.