To replace the time-consuming sample pretreatment procedure, a microfluidic chip-CE device incorporating on-chip sample desalting/preconcentration with transient isotachophoresis (ITP)/capillary zone electrophoresis (CZE) was fabricated to perform sequential on-chip sample pretreatment and CE determination of four urinary proteins in clinical samples. On-chip sample desalting, clean-up and analyte preconcentration enable removing interfering sample matrix prior to transferring analytes to separation capillary for transient ITP/CZE determination. Four important urinary proteins transferrin, beta 2-microglobulin, human serum albumin (HSA) and immunoglobulin G (IgG), investigated were shown to achieve quantitation limits sufficiently high to meet medical requirements, sensitivity enhancement up to 40-fold and detection limits down to 0.3, 0.05, 0.6, 0.5mg/L, respectively. Compared to the stacking effect, the use of a large sample size was found to be the major factor for sensitivity enhancement. The method reliability is established by close to 100% recoveries and statistical agreement of results from the method developed with currently used clinical radio-immunoassay method for all four proteins investigated. Moreover, an assay time of less than 10min is needed in the method developed as compared to 7h for the radio-immunoassay method.