The Human Microbiome Project (HMP) launched in 2008 by the National Institute of Health (NIH) fascinated microbiologists with discoveries of micro-organisms inside and outside of human beings. Their correlation with health and disease brings a new insight to preventive and therapeutic measures. At present, focus is more on the micro-organisms residing in the gut and various factors capable of altering their composition. The conclusion made by Dr. Edward Bach regarding the ability of homoeopathic potencies to alter bowel flora and its relation with chronic diseases was investigated and experimented way back. The present review attempts to correlate gut microbiota with the art and science of homoeopathy.