A rapid, reliable HPLC method with UV detection (240 nm) was developed and validated for quantitation of saquinavir in mice brain and testis. Saquinavir and the internal standard were isolated from homogenized tissue matrices using liquid-liquid extraction procedure and were then analyzed using an isocratic mobile phase by reversed-phase liquid chromatography. The lower limit of quantification was 50 ng/g for both brain and testis. A linear dynamic range of 50-5000 ng/g for both brain and testis was established. This HPLC method was validated with between-batch precision of 0.5-4.4 and 1.5-5.5% for brain and testis, respectively. The between-batch accuracy was 94.7-105.9% and 97.5-105.0% for brain and testis, respectively. The present method was applied for tissue distribution studies of the novel drug delivery systems of saquinavir in mice.