The Joint Workshop on "Automated Reasoning for Security Protocol Analysis and Issues in the Theory of Security" (ARSPA-WITS 2009) was held in York, UK, March 28-29, 2009, in association with ETAPS 2009. ARSPA is a series of workshops on "Automated Reasoning for Security P- tocol Analysis," bringing together researchers and practitioners from both the security andthe formalmethods communities,from academiaand industry,who are working on developing and applying automated reasoning techniques and tools for the formal speci?cation and analysis of security protocols. The ?rst two ARSPA workshops were held as satellite events of the Second International JointConferenceon Automated Reasoning(IJCAR 2004)andof the 32nd Int- nationalColloquiumonAutomata,LanguagesandProgramming(ICALP2005), respectively. ARSPA then joined forces with the workshop FCS (Foundations of Computer Security): FCS-ARSPA 2006 was a?liated with LICS 2006, in the context of FLoC 2006,and FCS-ARSPA 2007 was a?liated with LICS 2007 and ICALP 2007. WITSistheo?cialannualworkshoporganizedbytheIFIP WG1.7on"T- oretical Foundations of Security Analysis and Design," established to promote the investigation on the theoretical foundations of security, discovering and p- moting new areas of application of theoretical techniques in computer security and supporting the systematic use of formal techniques in the development of security-related applications. This is the ninth meeting in the series. In 2008, ARSPA and WITS joined with the workshop on Foundations of Computer - curityFCSforajointworkshop,FCS-ARSPA-WITS2008,associatedwithLICS 2008 and CSF 21.