In this work, we have investigated the effect of nanostructured surfaces on the attachment and viability of two bacterial species of medical relevance. Surfaces having squares, channels and dots in the nano size range with intermittent hydrophobicity and hydrophilicity showed complex effects on both live and dead E. coli cells. Nevertheless the behaviour of S. aureus was found to be less modulated by the surface properties. The square structures had promising repellent effect on both live and dead E. coli species while S. aureus populated these surfaces very well. On dot nanostructures the population by E. coli was considerably higher than on the surrounding spaces while the distribution of S. aureus cells remained uniform on both structured and unstructured areas. When the bacteria were applied to surfaces with channels, live E. coli cells showed a very interesting fluctuation in function depending on the width of the channels but this fluctuation was not observed in case of dead cells. Because of its spherical form, lacking flagellae and production of extracellular substances, S. aureus adhered to this structure more evenly and no fluctuation was observed. Strain specific bacterial physiology and reactivity to these surfaces may possibly also be a factor in influencing the interaction. These initial results contribute to the purposeful design of species-specific pro-or anti-bacterial surfaces for the use of lab-on-a-chip devices and various types of medical devices.