Probiotics, live microorganisms that offer various health benefits, have been widely studied for their potential to prevent and treat a range of conditions. However, recent evidence highlights several health risks associated with probiotics, including opportunistic infections, detrimental immunological effects, metabolic disturbances, allergic reactions, and the spread of antimicrobial resistance (AMR). This review aims to address these concerns by examining recent studies published within the last five years, prioritizing clinical studies, in vivo and animal models, in situ, in vitro, and in silico approaches. Opportunistic infections, such as sepsis, bacteremia, and fungemia, have been linked to specific probiotic strains, particularly in immunocompromised individuals. Probiotics can also cause localized infections like endocarditis and abscesses. In terms of immunological effects, probiotics have been associated with elevated risk of autoimmune disorders, including celiac disease and type 1 diabetes. Allergic reactions, including skin allergies, allergic rhinitis, and food allergies, have shown mixed results, with some studies indicating increased sensitization in high-risk individuals. Metabolic disturbances, such as defective lipid metabolism and insulin resistance, have not been effectively regulated by probiotics, and in some cases, have even exacerbated these conditions. Additionally, probiotics have been found to facilitate the transfer of AMR genes to host microbiota, potentially leading to the establishment of AMR reservoirs in natural environments. In vitro and in vivo studies have demonstrated the feasibility of ARG transfer from probiotic strains to pathogens, raising significant concerns about the potential for AMR spread. The review emphasizes the need for further research to clarify and address these adverse effects, ensuring the safe and effective use of probiotics in various applications.Probiotics, live microorganisms that offer various health benefits, have been widely studied for their potential to prevent and treat a range of conditions. However, recent evidence highlights several health risks associated with probiotics, including opportunistic infections, detrimental immunological effects, metabolic disturbances, allergic reactions, and the spread of antimicrobial resistance (AMR). This review aims to address these concerns by examining recent studies published within the last five years, prioritizing clinical studies, in vivo and animal models, in situ, in vitro, and in silico approaches. Opportunistic infections, such as sepsis, bacteremia, and fungemia, have been linked to specific probiotic strains, particularly in immunocompromised individuals. Probiotics can also cause localized infections like endocarditis and abscesses. In terms of immunological effects, probiotics have been associated with elevated risk of autoimmune disorders, including celiac disease and type 1 diabetes. Allergic reactions, including skin allergies, allergic rhinitis, and food allergies, have shown mixed results, with some studies indicating increased sensitization in high-risk individuals. Metabolic disturbances, such as defective lipid metabolism and insulin resistance, have not been effectively regulated by probiotics, and in some cases, have even exacerbated these conditions. Additionally, probiotics have been found to facilitate the transfer of AMR genes to host microbiota, potentially leading to the establishment of AMR reservoirs in natural environments. In vitro and in vivo studies have demonstrated the feasibility of ARG transfer from probiotic strains to pathogens, raising significant concerns about the potential for AMR spread. The review emphasizes the need for further research to clarify and address these adverse effects, ensuring the safe and effective use of probiotics in various applications.