Determining the cause of botulism in the honey samples has always been problematic because of its biological and biochemical characteristics, the level and dispersion method and the nature of matrix14. The results of our study confirm this claim. High honey viscosity due to high sugar level and the small amount of water results in uneven distribution of C. botulinum spores which significantly hinders preparation, processing and the use of honey samples by applying both conventional and molecular methods in laboratory diagnosis8. All this can lead to false negative results both using microbiological and molecular testing methods, especially in honey with low contamination levels which is confirmed by the studies of other authors. PCR has proven itself as a significantly more sensitive method for detection of C. botulinum spores in honey samples than cultural methods; however, PCR can produce false negative results.