In this article we describe methods and results of the interactions of selected proteins with selected nanoparticles. The method applied in order to investigate the impact of nanoparticles on the secondary structure of proteins is circular dichroism (CD) spectroscopy. It is shown that in the case of bovine serum albumin (BSA), the secondary α-helix structure is lost to a significant extent when silver or gold nanoparticles are added to the solution. This is explained by the formation of association complexes, the stability of which depends on whether or not the metallic surfaces are accessible to the protein. In the case of polymeric surfaces, these interactions are considerably weaker. In addition to CD spectroscopy, we have developed and applied Surface-Enhanced Raman Spectroscopy (SERS) for the investigation of the response of selected bonds of proteins in their interactions with nanoparticles. In the case of metallic nanoparticles, where the Raman signals are enhanced in the presence of nanoparticles due to the SERS surface effect, this enhancement can be used to identify the structural elements of the protein which are most affected by the interaction with the nanoparticles. The aim of this work is to identify the nature of protein/nanoparticle interaction and to describe how this depends on chemical and surface chemical composition of the nanomaterial, as well as on the size and composition of individual proteins. Ultimately we are aiming at developing a predictive tool for such interactions.