Methanolic extract of Capparis sinaica Veill was tested for its in vitro antiviral activity against highly pathogenic avian influenza strain H5N1 using plaque inhibition assay in Madin-Darby canine kidney. The results indicated that the extract possessed potent antiviral activity (100% inhibition at the concentration of 1 μg/ml). Based on this result, C. sinaica Veill was selected for further study by applying bioactivity-guided fractionation to isolate its antiviral principles. The fractions eluted with EtOAc and 25% MeOH in EtOAc were found to hold the antiviral activity. Further chromatographic separation of the fractions holding the antiviral activity led to the isolation of quercetin (1), isoquercetin (2) and rutin (3) for the first time from this species. The isolates showed reduction in the virus titre by 68.13%, 79.66% and 73.22% inhibition at a concentration of 1 ng/ml, respectively.