Natural Killer T (NKT) cells are a phenotypically and functionally diverse subset of T cells, which recognizes self- and microbial lipids in the context of the atypical MHC class I molecule CD1d. NKT cells exhibit potent effector functions and play critical roles in antimicrobial defense, cancer immunosurveillance and the modulation of immune-mediated disorders. Recent evidence has revealed extensive cross-regulation between the mucosal microbiota and CD1d as well as NKT cells. Microbial exposure at mucosal surfaces, particularly during early postnatal development, regulates NKT cell trafficking and function in the intestine and the lung and determines the susceptibility to NKT cell-mediated inflammatory disorders. Conversely, CD1d controls the composition of the intestinal microbiota; perhaps through the regulation of Paneth cell function. Here, we provide an overview of recent findings on the crosstalk between the microbiota and NKT cells and discuss the implication for mucosal homeostasis and its dysregulation in inflammatory disorders.