Experimental design and analysis is an effective and commonly used tool in scientific investigations and industrial applications. Many successful applications have been reported in engineering domains, such as chemical engineering, electrical engineering, and mechanical engineering. However, few cases have been reported in biological research, particularly in virology study. Antiviral drug combinations are increasingly used to reduce possible drug-resistant viral mutant and reduce cytotoxicity. Drug combinations have often been reported to have higher efficacy and lower individual drug dosage. However, the combined antiviral drug effect is generally hard to assess. One important reason is due to the complex interactions between biological systems and drug molecules. We report a study using fractional factorial designs to investigate a biological system with Herpes simplex virus type 1 and five antiviral drugs. The experiment uses a novel composite design that consists of a 16-run fractional factorial design and an 18-run orthogonal array. The results indicate that two chemical drugs, Ribavirin and Acyclovir, are more effective than three Interferon drugs. Furthermore, significant interactions exist within the Interferon drug group and within the Ribavirin-Acyclovir chemical drug group, but the interactions between the Interferon group and the chemical group are not significant. These observations have major implications in the understanding of antiviral drug mechanism towards better design of combinatorial antiviral drug therapy. Copyright © 2012 John Wiley & Sons, Ltd.