Mycotoxins are toxic secondary metabolites produced by a number of different fungi, and can be present in a wide range of food and feed commodities including cereal grains, oil seeds, dried fruits, apple juice, wine and meat products from animals fed contaminated meal. Many mycotoxins are highly resistant, and survive food processing, and therefore enter the food chain and provide a threat to human health. The optical waveguide lightmode spectroscopy (OWLS) technique has been applied to the detection of Aflatoxin and Ochratoxin in both competitive and in direct immunoassays. After immobilizing the antibody or antigen conjugate for the direct or indirect measurement, respectively, the sensor chip was used in flow-injection analyser (FIA) system. When using non-competitive method, sensor responses were obtained first only at analyte concentrations of 5-10 ng ml(-1). In both cases, the responses were very unstable. For competitive sensor investigation with the sensitized chip first the optimal dilution rate of monoclonal antibodies was determined, for the measurement of Ochratoxin A and Aflatoxin B1 the monoclonal antibody stock solution was diluted to 1 microg ml(-1) and to a 1:400 dilution, respectively. During the competitive measurement standard solutions were mixed with monoclonal antibodies at the appropriate concentration, the mixture was incubated for 1 min and injected into the OWLS system. The sensitive detection range of the competitive detection method was between 0.5 and 10 ng ml(-1) in both cases. After the establishment of the indirect method, barley and wheat flour samples were measured, and the results were in good correlation by those measured by enzyme linked immuno-sorbent assay (ELISA). Regression coefficient between the two methods for Ochratoxin and Aflatoxin was determined as 0.96 and 0.89, respectively.