The purpose of the current study was to examine potential routes of vaccine administration for the induction of antigen-specific responses in the genital tract of women. Sixteen women were enrolled in this study, and the level of influenza-specific antibodies induced in the genital tract was measured after rectal or intramuscular immunizations. Both methods of administration induced significant increases in the concentration of flu- specific IgA found in cervical secretions within 28 days after vaccination. Initially flu-specific IgG antibodies were not induced in the genital tract by either route. As expected both IgA and IgG flu-specific antibodies were dramatically increased in serum after intramuscular vaccination. In contrast, rectal administration did not induce significant IgA responses, and only small flu-specific IgG increases in serum. Six months after administration, IgA flu-specific antibody concentrations were significantly higher than baseline levels in vaginal secretions and saliva isolated from both subject groups and flu-specific IgG concentrations in cervical secretions were high in the rectal immunization group. The long-term presence of both IgG and IgA antibody in genital secretions suggests that rectal immunization may be an effective method for induction of immune protection in the genital tract of women.