Skin serves as a protective barrier against invasion by pathogens and harmful antigenic particles. Filaggrin is a key structural protein that facilitates terminal differentiation of the keratinocytes and formation of the skin barrier. Since the establishment of a sequencing method for the entire filaggrin gene (FLG) in 2006, approximately 40 loss-of-function FLG mutations have been identified in patients with ichthyosis vulgaris and/or atopic dermatitis (AD). Notably, there is a clear difference in filaggrin genetics between the European and Asian races. Overall, approximately 25–50% of AD patients have been found to harbor filaggrin mutations as a predisposing factor. In addition, filaggrin mutations are significantly associated with asthma. The restoration of skin barrier function seems a feasible and promising strategy for prophylactic treatment of AD patients with FLG mutations. This article reviews the discovery of filaggrin mutations; their association with AD, asthma and other atopic diseases; and FLG-related potential treatment strategies.