Introduction: Persistent human papillomavirus (HPV) semen infection is increasingly associated with male infertility. Adjuvant HPV vaccination is suggested to reduce the time to clearance and the disease relapse in males with persistent HPV semen infection. However, only a sub-population of patients show a clinical benefit from adjuvant vaccination. Here, we aimed to address the effectiveness rate of HPV adjuvant vaccination in males with genital tract infection and the possible prognostic markers of healing. Methods: Clinical records from 379 patients with persistent seminal HPV detection, all receiving HPV adjuvant vaccination, were considered. Clinical data, including genital HPV-DNA assessment by INNO-LiPA genotyping, semen HPV-DNA analysis by FISH analysis and serum antibody titer, were collected at basal (T0) and after 6 months (T1) since the vaccination cycle ended. Results: Clearance of genital HPV-DNA was recorded in 326 (86%) patients. Serum HPV-antibody titer at T1 was the most important prognostic factor associated with HPV-DNA clearance. A serum antibody titer equal to or greater than the threshold value 1:125, obtained by ROC curve analysis, was prognostic of healing. Conclusions: Anti-HPV antibody represents a suitable marker of adequate immune response to HPV vaccination in patients with genital infection.