The influence of non-thermostated capillary inlet on accuracy of data obtained by affinity capillary electrophoresis is examined in the case of kinetically labile systems (with fast kinetics of equilibrium) at different temperatures. The system uranyl-selenate is studied in aqueous perchloric acid solutions (pH 2.5, ionic strength 0.05 mol l−1) in the temperature range from 15 °C to 55 °C. Moving of the sample through the non-thermostated inlet into the thermostated region of the capillary is used in order to avoid the influence of non efficiently thermostated short capillary inlet. The data on mobility values of uranyl and the values of stability constants obtained by this mode are compared with the data obtained in a traditionally used mode (injection in non-thermostated inlet region). The uranyl mobility values obtained by the two methods are different at temperature higher than 35 °C. However, the difference between stability constants obtained by the two methods is not significant (ambient temperature is 20 °C).