When treating vaginitis, boric acid kills fungus, and acidophilus merely supports friendly bacteria levels that eventually restore bacterial balance to the vagina, thus overwhelming the fungus. Boric acid can irritate the skin, while acidophilus inserted into the vagina has no similar side effects, according to the Journal of Family Practice.
Vaginitis is an inflammation of the vagina caused by a disruption of vaginal bacteria. Candida, a yeast-like fungus, is the cause of approximately 40 percent of all vaginitis cases, repots the University of Maryland Medical Center. Candida grows naturally within the vagina, but certain risk factors encourage it to flourish to critical masses that lead to yeast infections. These factors include antibiotics, high sugar intake, tight clothing, noncotton underwear, birth control pills, HIV, sexually transmitted diseases, diabetes, pregnancy, menstruation, use of corticosteroids and obesity.
Another related difference between boric acid and acidophilus suppositories is their availability. Individuals seeking the former may have to fill empty capsules with boric acid, states WebMD. Acidophilus suppositories are available over-the-counter, as of 2015, states MedlinePlus.
A standard boric acid treatment entails inserting a size zero gelatin capsule filled with boric acid in the vagina at bedtime for 7 days, states WebMD. As of 2015, there is evidence that acidophilus suppositories containing at least 1 billion live, friendly bacteria inserted twice daily for 7 days improves symptoms associated with vaginitis, according to MedlinePlus.