In recent decades, science and food technology have contributed at an accelerated rate to the introduction of new products to satisfy nutritional, socio-economic and quality requirements. With the emergence of modern molecular genetics, the industrial importance of Saccharomyces cerevisiae, is continuously extended. The demand for suitable genetically modified (GM) S. cerevisiae strains for the biofuel, bakery and beverage industries or for the production of biotechnological products (e.g. enzymes, pharmaceutical products) will continuously grow in the future. Numerous specialised S. cerevisiae wine strains were obtained in recent years, possessing a wide range of optimised or novel oenological properties, capable of satisfying the demanding nature of modern winemaking practise. The unlocking of transcriptome, proteome and metabolome complexities will contribute decisively to the knowledge about the genetic make-up of commercial yeast strains and will influence wine strain improvement via genetic engineering. The most relevant advances regarding the importance and implications of the use of GM yeast strains in the wine industry are discussed in this mini-review. In this work, various aspects are considered including the strategies used for the construction of strains with respect to current legislation requirements, the environmental risk evaluations concerning the deliberate release of genetically modified yeast strains, the methods for detection of recombinant DNA and protein that are currently under evaluation, and the reasons behind the critical public perception towards the application of such strains.