The diverse collection of microorganisms colonising the healthy gastrointestinal tract of pigs, referred to as the microbiota, plays an essential role not only for the well-being of the animal, but also for animal nutrition and performance and for the quality of animal products. A number of naturally-occurring and artificial factors has been shown to affect the composition and activity of the microbiota in the gastrointestinal tract of pigs, these include: diet composition, growth promoting antibiotics, copper, use of probiotics, specific carbohydrates, organic acids and fermented feed. It is generally accepted that the microbiota in the small intestine competes with the host animal for easily digestible nutrients and at the same time produces toxic compounds. A pronounced microbial fermentation occurs in the stomach and small intestine in young piglets. Results have shown that approximately equal amounts of organic acids were produced in the three compartments: stomach, small intestine and large intestine. Further, experiments have shown that as much as 6% of the net energy in the pig diet could be lost due to microbial fermentation in the stomach and small intestine. On the other hand it has been shown that on a normal Danish pig diet, 16.4% of the total energy supply for the pig is achived from microbial fermentation in the large intestine. However, the microbiota in the gastrointestinal tract is unstable the first week after weaning and it takes 2 to 3 weeks after weaning before the fermentation capacity of the microbiota in the hindgut has developed. Use of growth promoting antibiotics in the feed is widespread in pig production. However, the use of the antibiotics avoparcin and virginiamycin as growth promoters in animal feed has been associated with an increase in resistance of bacteria to therapeutic agents and a fear that this could reduce the ability to treat diseased humans. This has caused an increased awareness of the use of antibiotics and a general wish to reduce the use of antibiotic growth promoters. Probiotics, organic acids and specific carbohydrates (yeast cell walls) are often suggested as alternatives to the use of antibiotic growth promoters. However, due to their relative high prices and the variability and unpredictability of their effect, the use of these products is financially questionable in practical pig production. One way to solve this problem may be the use of fermented liquid feed. Fermented liquid feed is characterised by a high number of lactic acid bacteria, high number of yeast and high concentration of lactic acid, and several investigations has shown fermented liquid feed to improve growth performance in pigs and to established a prophylactic barrier against gastrointestinal disorders. In general there is no doubt that the effect of feed additives are greatest in young animals where they have been found to improve growth performance and to reduce scouring and neonatal mortality. The present paper review our current state of knowledge about how various feed additives affect the gastrointestinal ecosystem.