Reliable response measurements are extremely important for proper bridge health monitoring but incomplete and unreliable data may be acquired due to sensor problems and environmental effects. In the case of a sensor malfunction, parts of the measured data can be missing so that the structural health condition cannot be monitored reliably. This means that the dynamic characteristics of natural frequencies can change as if the structure is damaged due to environmental effects, such as temperature variations. To overcome these problems, this paper proposes a systematic procedure of data analysis to recover missing data and eliminate the environmental effects from the measured data. It also proposes a health index calculated statistically using revised data to evaluate the health condition of a bridge. The proposed method was examined using numerically simulated data with a truss structure and then applied to a set of field data measured from a cable-stayed bridge.