The system comprises two flow injection-capillary electrophoresis interfaces into which the opposite ends of the separation capillary are inserted. The electrolyte solution flows through both interfaces by use of hydrostatic pressure. The injection of the samples into the electrolyte flow is accomplished by a rotary-type chromatographic valve at the grounded side and by a pinch-valve injector at the high-voltage side that provides sufficient isolation from the high electric field. The system allows a fully automated dual-injection sequence of samples from both capillary ends and simultaneous electrophoretic separation of anions and cations in the samples. The analytes are detected by a high-voltage contactless conductometric detector positioned approximately in the middle of the separation capillary. The parameters of the system were evaluated. The repeatability of the flow injection-capillary electrophoresis system for the simultaneous determination of anions and cations was evaluated for ten consecutive injections and relative standard deviation (RSD) values for peak areas were better than 1.0%. The sample throughput for total ionic analysis was estimated to be 25 samples per hour. The system was used for automated simultaneous analysis of anions and cations in various real samples. Using a short separation capillary, rapid total ionic analysis in less then 1 min is demonstrated.