Cyclosporine A (CyA) is a lipophilic oligopeptide that has a very limited solubility in water of only 0.008 mg/ml at ambient temperature. It has the ability to form inclusion complexes with cyclodextrin (CD) whose complexes can self-assemble to form aggregates. We have previously developed eye drops with CyA/CD aggregates. Our aim was to study cyclodextrin complexes of lysozyme, a small polar globular protein, and to compare the results with those obtained for CyA. We also wanted to test the stabilizing effect of CDs on lysozyme. Phase-solubility studies of various CDs were performed with CyA and lysozyme. Complexation and particle size measurements were made with dynamic light scattering (DLS) and UV. Solid drug fractions were determined. Thermal and chemical stability studies were performed on lysozyme in the presence of various CDs. Recovery of lysozyme activity in the presence of various CDs after a heat shock was determined. Both CyA and lysozyme are able to form non-inclusion complexes with CD and those complexes can self-assemble and form micro sized aggregates. In case of lysozyme the forces involved are relativity weak and the lysozyme/CD complexes dissociate upon centrifuging, however for CyA the aggregates are stronger and do not dissociate upon centrifuging. CyA is therefore suitable for eye drop preparations containing CDs for sustained drug release whereas lysozyme is not. This is mainly due to the fact that CyA forms inclusion complexes with CDs, whereas lysozyme is not able to do so due to its polar surface. The lysozyme/CD non-inclusion complexes can offer some protection against lysozymes chemical and thermal denaturation. CD can, however, form complexes with unfolded lysozyme and hamper refolding of the protein after heat shock.