Uncertainty is an existential phenomenon that lies in all human relations, will accompany the analysis and decisions taken in any security system. The most important and typical manifestations of uncertainty in security are: the dilemma of interpretation about motives, intentions and capabilities of other; and the dilemma of response related to the issue of how to respond to threats. The problem of uncertainty in the security systems generally is considered to be unsolvable even talk certainty of uncertainty, however, there are philosophical and empirical approaches and analytical methods for reducing uncertainty in the course of decision-making. The paper presents the theoretical aspects of uncertainty in security systems, discusses the meaning o f these dilemmas, and has potential for reducing extent of the problem.