The active ingredient in Betadine is iodine, and some research shows that it can be an effective antimicrobial. Keep in mind that allergic sensitivity to iodine is a possible concern with some individuals. Numerous high quality studies show the effectiveness of chlorhexidine as an antimicrobial agent. Chlorhexidine is likely one of the most researched antimicrobial agents available today. And while it has some drawbacks such as the propensity to stain teeth and an unfavorable taste, it works very well. Your best approach would be to formulate a clinical question and then do a PubMed search of the literature to determine which agent would work best for a particular patient. It's possible that you may want to use one agent for a certain patient and the other agent for another.