In the present report, we describe HPV type-specific prevalence in cervical samples from WLHIV from South Africa with different underlying, histologically confirmed stages of cervical disease, and explore a possible association with hypermethylation of host cell genes ASCL1, LHX8, and ST6GALNAC5. These genes were identified in a recent genome-wide methylation profiling study on HPV-positive self-collected cervico-vaginal specimens [26]. Here, LHX8 is linked to cervicitis.