An integrated optical Mach–Zehnder interferometer (IO-MZI) on silicon was specially designed and tested for application as an affinity sensor. In order to obtain the necessary sensitivity, an optimisation of the refractive index and the thickness of the waveguiding layer was carried out. Refractive measurements with ethanol/water mixtures show a sensitivity of about one order of magnitude higher than the IO-MZIs previously described. The compensation of unspecific protein interaction in an affinity sensor set-up was demonstrated by using both branches of the IO-MZI. One branch was coated with a antigenic structure and blocked with a protein mixture whereas the other was only blocked. A sample with a high background of serum proteins was applied and only the sample containing the specific antibody gave a measurable signal.