Childhood malnutrition is a global problem and one of the leading cause of stunted growth, and responsible for the death of millions of children every year. Although extensive efforts have been made to promote healthy growth but results are not satisfactory and infant's health remains a challenge. Previously, it was demonstrated that undernourished children have disrupted normal pattern of intestinal microbiota and led to a proposal that it might be involved in impaired postnatal growth. Recently, various research groups focused on Malawian population and proved the role of intestinal microbiota in the stunted growth of children. In addition, one group showed the role of sialylated bovine milk oligosaccharides in promoting microbiota-dependent growth in malnourished children. Moreover, it was also revealed that Clostridium symbiosum and Ruminococcus gnavus might be used as therapeutic agent for ameliorating growth abnormalities in malnourished children. The current article summarizes the recent advancement in identifying interventions regarding health promotion of malnourished children.