A new method is developed for the state estimation of linear time-varying discrete systems with unknown inputs. By making use of the two-stage Kalman filtering technique and a new proposed unknown inputs filtering technique, a robust two-stage Kalman filter (RTSKF) which is unaffected by the unknown inputs can be readily derived and serves as an alternative to the Kitanidis' unbiased minimum-variance filter. The application of this new filter is illustrated by optimal filtering for systems with unknown inputs.