Self-assembling peptide nanomaterials exhibit great potential in biomedical fields, especially for the delivery of various drugs and genes for treating disease therapy. This chapter introduces the design and synthesis of 3D peptide hydrogels for drug and gene delivery applications. The fabrication strategies of functional peptide hydrogels via both physical and chemical cross-linking are introduced, and functional tailoring of the self-assembling peptide hydrogels is discussed. In addition, the techniques on applying the synthesized peptide hydrogels for delivering different drugs and genes are demonstrated.