Background. Pandemic influenza vaccination rate amongst healthcare workers in England 2009/2010 was suboptimal (40.3%). Targeting medical students before they enter the healthcare workforce is an attractive future option. This study assessed the H1N1 vaccine uptake rate amongst medical students and factors that influenced this. Methods. Anonymised, self-administered questionnaire at a medical school. Results. The uptake rate amongst 126 medical students offered the vaccine was 49.2% and intended uptake amongst 77 students was 63.6%. Amongst those offered the vaccine, the strongest barriers to acceptance were fear of side effects (67.9%), lack of vaccine information (50.9%), lack of perceived risk (45.3%), and inconvenience (35.8%). Having a chronic illness (OR 3.4 (95% CI 1.2–10.2)), 4th/5th year of study (OR 3.0 (95% CI 1.3–7.1)), and correct H1N1 knowledge (OR 2.6 (95% CI 1.1–6.0)) were positively associated with uptake. Non-white ethnicity was an independent negative predictor of uptake (OR 0.4 (95% CI 0.2–0.8)). Students who accepted the H1N1 vaccine were three times more likely (OR 3.1 (95% CI 1.2–7.7)) to accept future seasonal influenza vaccination. Conclusion. Efforts to increase uptake should focus on routine introduction of influenza vaccine and creating a culture of uptake during medical school years, evidence-based education on vaccination, and improving vaccine delivery.