Microbes are present in many places in our body (the intestines, skin, reproductive organs), but the majority of them, which play the most important role, are those which reside in the gastrointestinal tract. It is known that the digestive tract of a foetus is sterile; however, after birth, the number of microorganisms in the neonate’s intestines grows rapidly. The colonisation of the gastrointestinal tract by bacteria is of fundamental importance to one’s future life. Particular attention is paid to the so-called health programming. It is believed that during the first 1,000 days of a child’s life (including foetal life, infancy and early childhood), it is possible to programme human metabolism through appropriate nutrition. Adequate nutrition during pregnancy, lactation and the first few years of a child’s life not only ensures appropriate weight gain and optimal nutritional status, but is also part of long-term health programming. Presumably, health programming also plays a role in the development of allergic diseases. Recent evidence indicates that the risk of atopy may be associated with intestinal dysbiosis; as a result, there has been a growing interest in the role of probiotics in the prevention of allergic diseases. The best documented practice is the preventative administration of probiotics to pregnant and nursing women, and to children in their first 6 months of life in order to reduce the rate of atopic dermatitis. Certain data also point to the role of probiotics in the acquisition of food tolerance. In addition, it is important that the probiotic administered be effective, since not every formulation present on the market guarantees the desired effect. The bacterial strains must be examined for their genome, catalogued in banks and marked with an appropriate identification number. It is only from such catalogued and well-studied strains that colonies for the most effective formulations can be grown. It is not quantity, but quality of the bacteria that ensures their effectiveness.