The present paper describes the development of a low cost, highly accurate low capacitance measurement system that can be used over a range of 0 – 400 pF with a resolution of 1 pF. The range of capacitance may be easily altered by a simple resistance or capacitance variation of the measurement circuit. This capacitance measurement system uses quad two-input NAND Schmitt trigger circuit CD4093B with hysteresis for the measurement and this system is integrated with PIC 18F2550 microcontroller for data acquisition purpose. The microcontroller interacts with software developed in the PC end through USB architecture and an attractive graphical user interface (GUI) based system is developed in the PC end to provide the user with real time, online display of capacitance under measurement. The system uses a differential mode of capacitance measurement, with reference to a trimmer capacitance, that effectively compensates lead capacitances, a notorious error encountered in usual low capacitance measurements. The hysteresis provided in the Schmitt-trigger circuits enable reliable operation of the system by greatly minimizing the possibility of false triggering because of stray interferences, usually regarded as another source of significant error. The real life testing of the proposed system showed that our measurements could produce highly accurate capacitance measurements, when compared to cutting edge, high end digital capacitance meters.