S. aureus has evolved strategies to manipulate host-pathogen interactions to its own ends, and avoid killing by professional phagocytes. It has been suggested that S. aureus can reside and survive inside professional phagocytes - mainly neutrophils and macrophages. Moreover, the intracellular environment, instead of being disruptive could constitute a beneficial 'niche'. My hypothesis is that S. aureus evade elimination by subverting one or more of uptake and intracellular processes. Internalisation and autophagy are host response processes already reported to favour pathogenesis of other bacteria. Widefield fluorescence and confocal microscopy has been used to track pathogens inside of the transparent zebrafish embryo. S. aureus strains were stained before injection with pH-sensitive and insensitive fluorescent dyes to assess the stage of endosome maturation by pH decrease. Transgenic zebrafish lines were developed during this study to specifically mark autophagosomes (LC3 fused with GFP and RFP). Nomarski DIC combined with high power fluorescence microscopy enabled imaging of pathogen uptake, phagocyte-to-phagocyte interactions and bacterial acidification in vivo. Results of whole body counts of bacteria internalised by phagocytes showed more intake into macrophages than into neutrophils. Quantification of bacteria labelled with pH sensitive bacterial cell wall dyes indicated different acidic conditions in bacteria-containing endosomes and lower acidification rates in neutrophils. Bacterial cells co-localise with LC3 protein in neutrophils. The presence of bacteria in LC3 tagged vesicles suggests that autophagy may be involved in S. aureus intake and intracellular processing. In vivo quantification combined with real time imaging have the potential to help increase our understanding of host - pathogen interactions at different stages of infection.