Systemic administration of antifungal agents for invasive mycoses has dramatically increased over the past 10 years in many fields of medicine. The increase has been due both to an increasing immune compromised population and to potent antibacterial agents which allow these fungi to invade tissue. It is apparent that our understanding of the use of both the old and new antifungal agents has significantly increased in the last few years. In this review, we attempt to document our extensive knowledge of the adverse effects of the polyenes, flucytosine, griseofulvin and azoles when given systemically for treatment. Interwoven in this documentation of the adverse reactions to these agents is the attempt to help clinicians potentially avoid some of these adverse effects and if they do occur, to be able to identify and successfully manage them.