Allicin has been shown in studies to have antifungal activity, however it is considered as an intermediate compound with short half-life, which will eventually transform into other more stable metabolites such as ajoene.

Naganawa et al (1986) first demonstrated antifungal activity of ajoene against Aspergillus niger and Candida albicans. In their study, it was shown that ajoene has superior antifungal activity against allicin. In investigating the activity against other fungal strains, ajoene also strongly inhibited the growth of Candida glabrata, C. tropicalis, Trichophyton mentagrophytes, Tricosporon beigelii and Saccharomyces cerevisiae.

Most topical fungal infections are not life threatening. However, a fungal infection can be systemic when the fungi enter the bloodstream and affect multiple body tissues and organs. An example is Scedosporium prolificans, an opportunist pathogen first described in 1984. It causes different types of infections in immunocompetent and immunosuppressed people and was found to be difficult to treat due to its resistance to most antifungal drugs. In 2003, Davis et al demonstrated potent in vitro antifungal effects on S. prolificans. Davis et al found that ajoene has effective antifungal effects against this strain of fungus.

In general, ajoene, which has shown its effective antifungal activity in vitro is postulated to be a natural substitute to synthetic antifungal drugs.