The adsorption behaviour of single molecules of a lumazine synthase/riboflavin synthase complex and of porcine circovirus on carbon, SiO and mica was studied by freeze drying and metal decoration. The orientation of the individual particles on the substrate was determined by cross-correlation of the metal distribution with molecular models at different orientations as well as by multivariate statistical analysis. A substrate-dependent preferential orientation of the individual particles was observed. On the surface of protein molecules, the contact areas to the substrate can be correlated with the atomic structure, if the latter is known from X-ray analysis.