This study examined the effect of an HIV vaccine on mucosal innate factor expression. Serum, gingival fluid, and genital mucosal secretions were collected from high-risk women and men enrolled in an HIV-1 efficacy vaccine trial and from low-risk women and men. Samples were tested by standard ELISA for lactoferrin, myeloid-related protein-8/14, and secretory leukocyte protease inhibitor. No consistent significant changes in innate factor levels were found in serum or secretions from vaccinees compared to placebo recipients or from high-risk compared to low-risk individuals. Because of the importance of innate immunity in host defense, evaluation of the mucosal innate immune system should be included in future HIV prevention trials.