The most common techniques used to study the immunological and microbiological factors of female genital tract are cervicovaginal lavage (CVL) and swabbing the cervix. As part of a comprehensive approach to different aspects of mucosal immunity, it is necessary to use techniques for the acquisition of a large number of information while using small amounts of samples. Thus, techniques such as transcriptomic analysis on microarrays, which can tell us about changes in thousands of genes, and the use of techniques for multiplex quantification of soluble factors (cytokines and soluble factors of immunity innate mucosal) must be adapted, tested and validated before the start of a vaccine trial so that the samples needed for immunological assessment be exploited optimally.