Natural phenolic compounds have been reported to directly inhibit influenza virus. Nonetheless, there have been no reports on the direct inhibitory effects of coffee ingredients. Here, we fractionated the hydrophobic and hydrophilic components of coffee. The hydrophobic fraction directly inhibited both a seasonal influenza A/Puerto Rico/8/24(H1N1) virus and a neuraminidase-resistant influenza A/Yokohama/77/2008(H1N1) virus infection in a dosedependent manner, while the hydrophilic fraction did not show any inhibitory effects, even at concentrations above 100 µg/ml. The HPLC profile of the hydrophobic fraction indicated that caffeine is the major component. Indeed, caffeine alone showed comparable anti-influenza virus activity. Interestingly, caffeic acid also inhibited viral infection, while chlorogenic acid, which is an ester of caffeic acid and (-)-quinic acid, showed no obvious antiviral effect at less than 2 mg/ml. We previously reported a method for enhancing the anti-influenza virus activity of epigallocatechin gallate, a major tea catechin, by lipase-catalyzed acylation. Using this methodology, we synthesized fatty acid esters of caffeic acid and evaluated their influenza virus-inhibitory effects. It was found that dioctanoyl ester of caffeic acid exhibited approximately 38-fold higher direct antiviral activity. To understand the essential structure required for virus inhibition, we further examined the antiviral activity of natural flavonoids containing either the caffeic acid skeleton or its analogous structure. Flavonols (quercetin, myricetin and morin) and hexahydrobenzophenone containing extended planar pi-conjugated systems efficiently inhibited the virus infection. Flavonoids possessing both radical scavenging activity and cytotoxicity tended to show higher antiviral activity, probably due to their affinity with viral surface factors. On the other hand, there was no apparent correlation between their antiviral activity and antioxidative activity. These findings provide insight into the design of anti-influenza virus agents from natural polyphenols.