Lichen planopilaris (LPP) is the prototype of cicatricial alopecia and is the follicular form of lichen planus. Some studies showed viral agents such as hepatitis C virus; Epstein Bar virus and human Herpes viruses are associated with classic and oral lichen planus. We conducted this study to find if there is a relationship between LPP and human herpes virus-6 (HHV-6) as this virus is prevalent worldwide. This cross-sectional study was conducted in Razi Hospital, Tehran, during one-year interval. Total of 30 treatment naïve LPP patients and 30 healthy matched controls enrolled the study. Serum anti-HHV-6 antibody and the presence of virus genome examined using ELISA and Nested PCR technique, respectively. HHV-6 genome was also determined three months after treatment in LPP patients. Twenty-nine (96.6%) and 3(10%) of LPP patients were positive for anti-HHV-6 antibody and DNA genome, respectively; while 28(93.3%) and 3(10%) were positive in the control group. The presence of anti-HHV-6 antibody and HHV-6 genome was not statistically different between LPP patients and controls (p value >0.05). The comparison between LPP cases after three months of systemic therapies and the same controls also showed no statistically significant difference (P value >0.05). This study showed there is no association between lichen planopilaris and HHV-6.