Probiotics are defined as live microorganisms which, when provided in sufficient amounts, have a beneficial effect on human health. In the last two decades, worldwide interest in the use of functional foods containing probiotic bacteria for disease prevention and health promotion has increased significantly, revealing new possible indications for the use of specific probiotic strains. On the other hand, increased probiotic use necessitates the need for accurate surveillance, not only for their effect, but also for their safety. Taking into account that probiotics are live microorganisms that can influence the human immune system, several safety issues need to be addressed. These include the potential for transmigration causing bacteremia and sepsis, the potential for antibiotic resistance, and other adverse effects such as those that might influence gastrointestinal physiology or immunological function. The aim of this review is to summarize available data on the safety of probiotics for human use.