In order to gain more information about local humoral immune responses to HPV infection, we quantified IgG, IgM, secretory-IgA (S-IgA), and total-IgA by ELISA, and lysozyme and lactoferrin by TR-IFMA, in cervical and cervicovaginal secretions of 40 healthy women and 28 high-risk HPV infected patients (11 were HPV16+). IgG, total-IgA, and S-IgA concentrations in cervicovaginal secretions (p < 0.0001) and high IgG and total-IgA concentrations (p < 0.001 and p < 0.01, respectively) in endocervical secretions were significantly higher in HPV+ patients than in the healthy group. Since the S-IgA/total-IgA ratio was significantly lower in cervicovaginal (7.5%) and endocervical secretions (36.5%) in HPV+ women compared to the control group (p < 0.003 and p < 0.001, respectively), HPV could be responsible for an increase in local production of non-secretory IgA (monomeric and dimeric forms). IgG and total-IgA concentrations in cervicovaginal and endocervical secretions fell in the same general percentage range in both HPV16+ and HPV+ groups (80% and 15%, respectively). However, the S-IgA/total-IgA ratio was much lower in HPV16+ than in HPV+ women, in both cervicovaginal secretions (3.4%) (p < 0.003) and in endocervical secretions (23.3%) (p < 0.001). Innate immunity proteins and local S-IgA response could not stop the spread of HPV infection in spite of high lysozyme and lactoferrin concentrations. HPV16+ disturbed the local humoral immune system, which could partly explain its low clearance.