There are numerorus published and ongoing experimental/clinical studies about probiotics and prebiotics, intestinal microbiota and nutrition. Three years ago, at the first International Symposium of Probiotics Prebiotics in Paediatrics in Istanbul (2012) we highlighted the 'paediatric perspective' on these issues and brought together more than 40 global key opinion leaders and 400 attendants to have a chance to extensively discuss the past, present and the future. In 2014, the second state of art congress, held in Antalya, aimed to discuss the gut microbiota and microbiotics and their impact through lifespan. Selected papers of this conference are presented in this special issue 'prebiotics and probiotics in paediatrics' of Beneficial Microbes. A summary of the conference results is provided below.