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The rapid increase of HIV-1 prevalence among Chinese men who have sex with men (MSM) provides an impetus for the acquisition of molecular epidemiologic information from this population. We conducted four serial crosssectional surveys during the years 2005-2009 and observed that the composition of HIV-1 subtypes was dynamically changing from clade B to CRF01_AE from years 2005-2009. HIV-1 infection in this population includes the persistent circulation of multiple HIV-1 subtypes and complex new recombinants.