In solid organ transplanted patients, annual influenza immunization is strongly recommended because of morbidity and mortality of influenza infections. In 2009, the rapid spread of a novel H1N1 influenza A virus led to the accelerated development of novel pandemic influenza vaccines. In Switzerland, the recipients received one dose of seasonal influenza and two doses of AS03-adjuvanted H1N1 vaccines. This situation provided a unique opportunity to analyze the influence of novel adjuvanted influenza vaccines on the production of de novo anti-HLA antibodies. We prospectively followed two independent cohorts including 92 and 59 kidney-transplanted patients, assessing their anti-HLA antibodies before, 6 weeks and 6 months after vaccination. Sixteen of 92 (17.3%) and 7 of 59 (11.9%) patients developed anti-HLA antibodies. These antibodies, detected using the single antigen beads technology, were mostly at low levels and included both donor-specific and non-donor-specific antibodies. In 2 of the 20 patients who were followed at 6 months, clinical events possibly related to de novo anti-HLA antibodies were observed. In conclusion, multiple doses of influenza vaccine may lead to the production of anti-HLA antibodies in a significant proportion of kidney transplant recipients. The long-term clinical significance of these results remains to be addressed.