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Voice over IP (VoIP) is the technology used to transport real-time voice over a packet-switched network. This study analyses the effects of encrypted VoIP streams on perceived Quality of Experience (QoE) from a user's perspective. An in-depth analysis on how the transparent nature of encryption can influence the way users perceive the quality of a VoIP call have been investigated by using the E model. A series of experiments have been conducted using a representative sample of modern codecs currently employed for digitising voice, as well as three of the most commonly used iterative block ciphers for encryption (DES, 3DES, AES). It has been found that the Internet Protocol Security encryption of VoIP strongly relates to the payload sizes and choice of codecs and this relationship has different effects on the overall QoE as measured by the E model, in terms of the way that users perceive the quality of a VoIP call. The main result of this paper is that the default payload shipped with the codecs is not the optimal selection for an increased number of VoIP calls, when encryption is applied and a minimum level of QoE has to be maintained, per call.