The main objective of this paper was to improve the efficiency of capillary electrophoresis-electrospray-mass spectrometry (CE-ESI-MS) interface by its miniaturization and optimization of controlling parameters. An ESI interface provides several functions: the transfer of analytes from the separation capillary into the MS orifice; mixing with a spray liquid; pressure control of flow through the spray capillary; control of the electrical potentials for CE separation and stable ESI. It follows that the construction and optimization of the interface is not a trivial task. To understand the function of the device properly, we investigated the effect of all working parameters on the overall analyte transfer. A separate task is the analysis of an effect of aerodynamic focusing on the behavior of sprayed particles moving into MS sampling orifice. The results of the mathematical modeling reveal the role of the electric field strength inside the separation capillary, pressure exerted on the interface, width of the gap between the separation and spray capillaries and aerodynamic focusing of sprayed analytes on their effective transfer. An integrated CE-ESI-MS device with miniaturized liquid junction interface was developed and optimized for the use with nano-electrospray needles. The interface was made from polysulfon with a spray capillary of 10 micrometers i.d. and 20 - 100 micrometers gap width between the separation and spray capillaries. An improved function of the device, verified under optimum conditions, enabled to reach limits of detection as low as units of ng/mL for biologically relevant components of various clinical samples. The examples of separations and identifications of carbohydrates will demonstrate an improved sensitivity and resolution reached by the microfluidic interface.