Influenza A/H1N1 new vaccine helps control disease spread. Cross-sectional survey was conducted at PHC & Emergency Departments in Qatar to determine influenza A/H1N1 vaccination rate among HCWs and associated factors, 523 HCWs were enrolled. The study showed that 13.4% HCWs received vaccination. Feeling protected strongly influenced vaccination decision (OR = 14.5). Uncertainty about vaccine efficacy and fear of side effects strongly influenced decision to reject the vaccine (OR = 0.3 and 0.2 respectively). Vaccination coverage was very low. The most common barriers were uncertainty about vaccine efficacy and fear of side effects. Health authorities should build message highlighting how the benefit of vaccination outweighs risk.