In the past few years, atomic force microscopy (AFM) has provided novel information on the ultrastructural and nanomechanical properties of yeast cell walls that play a major role in determining the flocculation characteristics of the yeasts. In this study, we used AFM to visualize at the nanoscale the cell surface topography and to determine cell wall nanomechanical properties (e.g. elasticity) of different strains of S. cerevisiae employed for brewing, winemaking and fuel alcohol production. Cell surface topography was found to correlate with the flocculation behaviour of these strains during their late stationary phase, with the cell surface of flocculent cells being rougher than that of weakly flocculent cells. The elastic modulus of the yeast cell walls showed that weakly flocculent strains had a more rigid cell wall than highly flocculent strains. This difference in elasticity seemed to have an effect on the adhesive properties of the yeast cell walls, with weakly flocculent yeasts displaying higher adhesion energy than the highly flocculent strains. These findings seem to indicate that yeast cell surface nanomechanical properties play an important role in governing flocculation.