Herpes simplex virus type 1 (HSV-1) is known to cause diseases of various severities. There is increasing interest to find drug combinations to treat HSV-1 by reducing drug resistance and cytotoxicity. Drug combinations offer potentially higher efficacy and lower individual drug dosage. In this paper, we report a new application of fractional factorial designs to investigate a biological system with HSV-1 and six antiviral drugs, namely, interferon alpha, interferon beta, interferon gamma, ribavirin, acyclovir, and tumor necrosis factor alpha. We show how the sequential use of two-level and three-level fractional factorial designs can screen for important drugs and drug interactions, as well as determine potential optimal drug dosages through the use of contour plots. Our initial experiment using a two-level fractional factorial design suggests that there is model inadequacy and that drug dosages should be reduced. A follow-up experiment using a blocked three-level fractional factorial design indicates that tumor necrosis factor alpha has little effect and that HSV-1 infection can be suppressed effectively by using the right combination of the other five antiviral drugs. These observations have practical implications in the understanding of antiviral drug mechanism that can result in better design of antiviral drug therapy. Copyright © 2012 John Wiley & Sons, Ltd.