The methodological framework of the Level 2 PSA appears to be currently standardized in a formalized fashion, but there have been different opinions on the way the sources of uncertainty are characterized and treated. This is primarily because the Level 2 PSA deals with complex phenomenological processes that are deterministic in nature rather than random processes, and there are no probabilistic models characterizing them clearly. As a result, the probabilistic quantification of the Level 2 PSA CET / APET is often subjected to two sources of uncertainty: (a) incomplete modeling of accident pathways or different predictions for the behavior of phenomenological events and (b) expert-to-expert variation in estimating the occurrence probability of phenomenological events. While a clear definition of the two sources of uncertainty involved in the Level 2 PSA makes it possible to treat an uncertainty in a consistent manner, careless application of these different sources of uncertainty may produce different conclusions in the decision-making process. The primary purpose of this paper is to characterize typical sources of uncertainty that would often be addressed in the Level 2 PSA and to provide a formal guidance for quantifying their impacts on the PSA Level 2 risk results. An additional purpose of this paper is to give a formal approach on how to combine random uncertainties addressed in the Level 1 PSA with subjectivistic uncertainties addressed in the Level 2 PSA.