Two-factor authentication with biometrics and smart-cards enabled by semi-fragile watermarking is proposed. Several advantages of the scheme as compared to earlier approaches are discussed and experiments for an iris-based recognition system demonstrate that semi-fragile integrity verification can be provided by the system. This is achieved without impact on recognition performance, since the slight degradation in terms of ROC behavior which is observed on the watermarked sample data is more than compensated by the additionally available template that is transferred from the smart-card to the matching site via watermarking technology.