Intestinal health is important for maximising the health, welfare, and performance of poultry. In addition, intestinal health issues in poultry can have devastating financial impacts for producers, and food safety concerns for consumers. Until recently, intestinal health issues were seen as a handful of known infectious agents leading to a set of severe and identifiable named diseases. There is however an emerging area which depicts intestinal health as a more complex and multifaceted system than previously known. Recent progress in technology suitable for microbial community analysis has evolved our understanding of the chicken intestinal microbiome. It is now understood that shifts in the composition of microbial communities can occur. These shifts can result in a series of implications, including: disease, welfare, environmental, and food safety concerns. Minor shifts in intestinal microbial balance can result in a wide continuum of disease presentations ranging from severe to mild clinical, subclinical or asymptotic. Differential diagnosis of poultry intestinal health issues may be challenging and is important for applying appropriate treatment options. This review discusses new and emerging topics in broiler chicken intestinal health, with a focus on microbial composition, newly discovered microbial shifts in classical poultry diseases, range in severity of enteric diseases, newly identified organisms in normal intestinal flora, implications of shifts in intestinal microbial communities and diagnosis of emerging intestinal health issues in poultry.