The major purpose of the presented study was to develop and to evaluate a flow cytometry-based assay (IIFC) for the determination of autoreactive antibodies in sera from canine cancer patients. A blinded study demonstrated the poor reproducibility of the standard, slide-based and microscopically evaluated indirect immunofluorescence test (IIF), especially with sera displaying a cytoplasmic reactivity. In the IIFC, the intra assay coefficient of variance ranged between 5% and 11%, the inter assay variance between 8% and 25%. The IIFC resulted in significantly less positive results among canine cancer patients (16%) than the IIF (40%). The latter results were due to low titered sera indicating that the standard assay may lead to a high proportion of false positive results. The limitation of the IIFC is that no conclusions can be made about the sub cellular localization of the fluorescence. However, this cytometry-based assay makes a more objective and standardized detection of canine autoreactive antibodies possible.