Systems biology represents a novel approach to comprehensively study the human immune response to vaccines at the global transcriptional and proteomic level. However, most systems vaccinology approaches utilize total PBMCs in their analyses. In this context, responses of under-represented immune cell types in the blood are potentially obscured by the predominant cells in the PBMC fraction, and the contribution of PMNs is completely ignored. To investigate the contribution of individual cell types in the immune response following vaccination, we developed a rapid and efficient method for purifying large numbers of T cells, B cells, monocytes, NK cells, myeloid DCs and neutrophils from fresh venous human blood for systems vaccinology studies. This optimized protocol was applied to adult volunteers vaccinated with 2011-12 seasonal TIV. 100mL blood was obtained prior to and on days 1, 3, and 7 post-vaccination. Whole blood, PBMC and PMN fractions were subjected to phenotypic analysis by flow cytometry. Immune cells were fractionated and processed for RNA and protein extraction in a single day. RNA-Seq and quantitative proteomics were performed on purified cells in order to determine individual expression profiles. Our results show significant variation in the phenotypes and expression profiles of immune cells at each time point. This innovative systems approach is currently being utilized to evaluate vaccine safety and efficacy in an adjuvanted influenza clinical trial.