The host–vector–pathogen interactions are governed since their origin by a subtle balance between attack and transmission strategies and defense mechanisms. Dialogs and conflicts are established between a molecular pathogen, potentially synergized by the molecular arsenal of an arthropod vector, and its host and will generate a mutual selection pressure which will result in profound changes in gene expression. In the postgenomic era, proteomics is now in its teenage but represents a promising tool to fill the blanks that still exist in biology despite the sequencing of the genomes of many organisms, but with databases to consolidate. In this chapter, we present the interest of proteomics in a better understanding of host–vector–pathogen crosstalk, through a synthetic review of the available analytical technologies and data generated by proteomics studies, discussing the pitfalls of current approaches, and presenting new approaches to decipher from molecular interactions to population proteomics leading to biomarkers discovery for diagnosis, therapy, and vaccine purposes.