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IEEE 802.1x and authentication server based security protocols are mainly used for enhancing security of wireless networks. We specify PAP and EAP-MD5 based security protocols formally with Casper and CSP, and then verify their security properties such as secrecy and authentication using FDR. We also show that they are vulnerable to the man-in-the-middle attack. Finally we discuss their security weakness and potential countermeasures related to PAP and EAP-MD5 protocols.