Background: Due to the high cost, subject availability and ethical constraints, it is often critically important in pre-clinical and clinical studies to carry out an adequate statistical analysis of longitudinal multivariate data over several time-points in trials in several small groups. Objectives: We aim to accurately assess and develop an appropriate distribution-free longitudinal model for an estimate of the comparative treatment effects of several biological factors in several small groups even if data sets should contain outlier measurements and censored values. This approach is used to evaluate the relative efficacy of mucosal and subcutaneous polypeptide vaccines in rhesus macaques exposed to SHIV. Study design: The algorithms of the non-parametric repeated measures ANOVA models are described, programmed and assessed. Biological Results: Using nonparametric ANOVA tests, we provided statistical evaluation of the relative efficacy of mucosal and subcutaneous synthetic! HIV/SIV peptide vaccines in rhesus macaques mucosally exposed to pathogenic SHIV-Ku2. We demonstrated with statistical significance that during the chronic phase of mucosal SHIV-Ku2 infection in immunized macaques, the numbers of the CD4(+) and CD8(+) cells reciprocally reflect the virus titers in plasma and both immune markers demonstrate better protection against pathogenic SHIV-Ku2 in intrarectally immunized MamuA*01 macaques. Conclusion: Despite limited data, our analysis shows better preservation of both CD4(+) and CD8(+) cells in intrarectally immunized animals. Our analytical methodology can be applicable in comparative estimates of the different treatment-associated effects and their synergy for a variety of longitudinal data sets (laboratory data, microarray data, clinical information) in small treatment groups, even if data sets contain outlier measurements and censored values.