Security is one of the principal and continuing concerns that restrict customers and organizations engaging with e-commerce. The aim of this paper is to explore the perception of security in e-commerce B2C and C2C websites from both customer and organisational perspectives. It explores factors that influence customers- perceptions of security. It also highlights conflicts between customer concerns with respect to security and those of an organization; existing research has not highlighted this issue greatly. This research provides a better understanding of customer needs and priorities on the subject of security, and enriches the currently available security perception literature, by providing new insights from empirical research conducted in Jordan. A qualitative research approach was adopted, since the research seeks an understanding of human (i.e., customer and organisational employee) perceptions.