In order to prevent power system blackout, and enhance system reliability, various forms of special protection systems (SPS) and defense plans have been implemented by utilities around the world. One of the main concerns in the design of an SPS is to assure whether the system could fit with the reliability specification requirements. The failure of SPS to detect the defined conditions and carry out the required actions, or to take unnecessary actions, could lead to serious and costly consequences. Thus, a quantitative reliability assessment for SPS is important and necessary. Using a single point value for the parameter to evaluate the reliability of SPS might give incomplete information about the system reliability due to the uncertainty of reliability model and input data. When a review study suggests that some modifications of the existing scheme are necessary, the sensitivity analysis techniques could provide the tools to do this investigation to identify the most significant components that have essential effects on the reliability of the SPS. In this dissertation, by incorporating an interval theory, a risk reduction worth importance concept, and a probabilistic risk-based index, a procedure is proposed to conduct parameter uncertainty analysis, identify critical factors in the reliability model, perform probabilistic risk assessments (PRA) and determine a better option for the refinement of the studied SPS decision process logic module. One of the existing SPSs of Taipower systems is used to illustrate the practicability and appropriation of the proposed design refinement procedure. With the advent of deregulation in the power industry, utilities have experienced a great pressure to fully utilize their current facilities to the maximum level. SPSs are often considered as a cost effective way in achieving this goal. This dissertation also presents a framework for quantitative assessment of the benefits and risks due to SPS implementation. Changes in energy, spinning reserve and customer interruption costs resulting from SPS operations are evaluated and risks of SPS operations and system security are assessed. The proposed methodologies are useful for power system planners and operators to evaluate the value and effectiveness of SPS for the remedy of transmission congestion and reliability problems.