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We present the introduction of a new generation of techniques for early and specific diagnosis of inflammatory, immune and degenerative eye diseases. We concentrate on the applications of the SELDI-TOF (Surface enhanced laser desorption ionisation - time of flight) mass spectroscopy in combination with molecular modelling and visualization for the analysis of the aqueous humour. For our study we used aqueous humour from 25 patients undergoing cataract operation. SELDI-TOF consists on one part of an apparatus allowing the laser bombarding of molecules on a solid surface and on the other part on a system which measure the time of flight of the molecules. During the measurement the molecules are liberated from the matrix and carried to the detector. Specific proteins can be identified by the characteristic peaks of the spectrogram. Albumin and gamma-globulin were found to a considerable extend in the aqueous humour. An increased amount has been detected in inflammatory humour. The quantity may reflect some underlying complications such as inflammation and animate for further research on the spectrum of proteins and peptides released by underlying eye disorder. SELDI-TOF delivers characteristic peptide mass fingerprints, which can be used as input for the prediction of the tertiary protein structure with homology modelling. Structural deviations between a genuine protein and a mutated can be an indicator about the underlying disease, paving the way for successful diagnostic and therapy. The combination of two new technologies namely SELDI-TOF and molecular modelling may offer a broad spectrum for the differential diagnosis of some eye diseases.