Probiotics are live microorganisms that can have a positive effect on the health of the host. The number of studies on genetically modified (GM) probiotics in recent decades is growing. The influence of GM probiotics on the treatment of elevated cholesterol, dental plaque and their anticancer activity is being intensively examined. Genetic engineering has enabled the creation of completely new probiotic mechanisms, the creation of recombinant probiotics such as Escherichia coli whose role is to sequestrate Shiga toxin from the body. Recombinant Streptococcus mutans BCS3-L1 showed its effect on caries treatment. GM probiotics (for example Lactobacillus zeae) showed positive results in producing antibodies whose main role is to act on pathogens, toxins, cytokines, and other agents in the body. Recombinant Lactococcus lactis might be a solution to the enzyme deficiency and might play a main role in the treatment of ulcerative colitis. All these studies have been carried out on experimental animals and are still waiting for the confirmation of their safety and efficacy in clinical trials on humans. The safe usage of GM probiotics is one of the main factors that should be considered because of its possibility to interact with immune system.