We estimated the vaccine effectiveness (VE) of trivalent and monovalent influenza vaccines, respectively, against laboratory-confirmed influenza infections in patients with influenza-like illness who visited physicians participating in the Bayern Influenza Sentinel in Bavaria, Germany during 2010/2011. Swab specimens were analysed for influenza A(H1N1)pdm09, A(H3) and B by PCR. VE was estimated using the test-negative case-control study design and logistic regression. In total, 1866 patients (790 cases, 1076 controls) were included. The VE of trivalent vaccines administered in season 2010/2011 against laboratory-confirmed infection with any influenza virus, adjusted for age group, sex, chronic illness and week of arrival of the specimen, was 67·8% [95% confidence interval (CI) 39·2–82·9)]. The adjusted VE of monovalent influenza vaccines administered in season 2009/2010 against laboratory-confirmed influenza A(H1N1)pdm09 infection in 2010/2011 was 38·6% (95% CI −70·0 to 77·8). This is the first VE study conducted in Bavaria. We concluded that the trivalent influenza vaccines were effective in our study population.