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The characteristics of bias caused by split-flow electrokinetic injection (SEKI), a new type of sample injection method used in coupled flow injection-capillary electrophoresis system (FI-CE), was investigated using pseudoephedrine hydrochloride, a basic drug, and ibuprofen, an acidic drug, as model analytes. It was found that bias imposed by SEKI under the condition of continuous sample matrix/running buffer was similar to that done by electrokinetic injection (EKI). The linearity of calibration curve provided by SEKI was similar to that offered by non-bias hydrodynamic injection (HDI) but significantly better than that obtained by EKI. These features were exploited to improve analytical performances in simultaneous determination of the minor ingredient of pseudoephedrine hydrochloride and the major ingredient of ibuprofen in a pharmaceutical preparation. Detectability of 0.7 mg/l for pseudoephedrine hydrochloride was achieved at a sample throughput rate of 24 times per hour, which is 30% lower than that obtained by HDI-based conventional CE. Relative standard deviations (RSDs) of 2.8% for the minor ingredient and 1.2% for the major ingredient were produced in 11 runs of a test solution containing 13.1 mg/l pseudoephedrine hydrochloride and 81.4 mg/l ibuprofen. This is an improvement compared to that obtained by HDI-based conventional CE. Analytical results for two batches of compound ibuprofen tablets by the SEKI-based FI-CE approach were in good agreement with that obtained by a conventional high performance liquid chromatographic method.