- Background Influenza vaccination is the most efficient and cost-effective method to prevent influenza. To increase vaccination coverage, health authorities use various intervention programs (IPs), such as cost subsidies or placing vaccination centers in malls to make vaccination more accessible. Nevertheless, vaccination coverage has been sub-optimal in most developed countries, including in Israel. Methods To determine possible drivers of individual vaccination uptake and to examine the effectiveness of different IPs in increasing vaccination, we analyzed a telephone survey of a representative sample of the Israeli population conducted in March 2011 (n = 470), and paper questionnaires at the work place and at homes during April-July 2011 to several sub-populations : soldiers (n = 81), medical staff (n = 107), ultra-orthodox Jews (n = 72), Israeli Arabs (n = 87) and students (n = 85). Results The population can be stratified into three sub-groups: Acceptors, who receive vaccination regardless of IPs (22%), Conditional Acceptors, who are only vaccinated because of IP implementation (44%) and Non-Acceptors, who are not vaccinated despite IP implementation (34%). Our analysis shows that the risk perception towards influenza relative to vaccination is higher in the Acceptors than in the Conditional Acceptors, with the Non-Acceptors showing the lowest risk perception (P < 0.01). For Conditional Acceptors, physician recommendation is the most effective IP, regardless of the sub-population tested (P = 0.04). Students and low-income participants were more prone than any others to be persuaded to receive vaccination following IPs. In addition, financial incentives were more effective for ultra-religious orthodox Jews and students; vaccinations in more accessible areas were more effective for the ultra-religious orthodox, soldiers, and medical personnel; and TV and radio advertisements were more effective for people above 50 relative to other age groups. Conclusions Risk perception of influenza and vaccination governs the likelihood of successful implementation of IPs. Policy makers in Israel should invest efforts to increase the knowledge regarding influenza and vaccination, and should apply specific interventions customized to the preferences and diverse perceptions among the Israeli sub-populations.