The assessment of biomaterial susceptibility to infection relies mainly on the analysis of macroscopic bacterial responses to material interactions, usually under static conditions. However, new technologies permit a more profound understanding of the molecular basis of bacteria-biomaterial interactions. In this study, we combine both conventional phenotypic analysis - using confocal microscopy - and genotypic analysis - using the relative reverse transcription polymerase chain reaction (RT-PCR) - to examine the interaction of bacteria with OH- and CH3-terminated glass surfaces, under dynamic flow conditions. Bacterial adhesion, as well as slime production and biofilm formation, was much higher on the CH3-terminated than on the OH-terminated glass - for four Staphylococcus epidermidis strains. This was in agreement with the icaA and icaD gene expression results that showed increased expression for the bacteria adhering to the CH3-terminated substrate, especially under the higher shear rate. Therefore, the combined effect of the surface chemistry and shear significantly influence the adhesion and phenotype of interacting bacterial cells, while there are putative links between phenotypic responses to bacteria-material interactions and gene-expression profile alterations. This indicates that analysis of gene expression not only can greatly refine our knowledge of bacteria-material interactions, but also yield novel biomarkers for potential use in biocompatibility assessment.