Potential residues of the potent allergen lysozyme used as a microbial stabilizing agent in wine production might pose a serious health thread to susceptible individuals. Therefore, EU legislation requires the labeling of the allergenic agent, if it is present in the final product. To allow for product testing, an indirect ELISA method to be specifically used in wine analysis was developed and validated. Furthermore, trial wines treated with defined amounts of lysozyme were subjected to an array of different filtration and other enological processing regimes in order to evaluate their potential to deplete the allergen content of the wines. By these means, processing methods ought to be identified that can be integrated in a good manufacturing practice guideline to enable wine producers to utilize lysozyme in their cellars and still provide wines free of allergenic residues. However, among the enological procedures under scrutiny, only bentonite fining proved to be capable of significantly reducing the allergenic residues.