In summary, we have demonstrated new methods for fabri-cating 3D nanofiber assemblies with gradients in structure and composition. The 3D nanofiber scaffolds with gradients in pore sizes were created by controlling the expansion rate of different regions of 2D nanofiber mats by blending various amounts of pluronic F-127. The dual gradients in pore sizes and fiber organi-zations from random, to partially aligned, and to aligned were formed by expanding 2D mats consisting of nanofiber layers sequentially deposited onto the mandrel with gradually increasing rotating speeds. In addition, the compositional gradients on 3D nanofiber assemblies were prepared based on the diffusion and encapsulation. We also demonstrated that dense regions of expanded scaffolds with graded pore sizes can greatly enhance the expression of hypoxia-related markers and chondrogenic differentiation of BMSCs, and bFGF gradients on 3D radially aligned nanofiber scaffolds can significantly accelerate the migra-tion of human dermal fibroblasts. The 3D nanofiber assemblies with gradations in structure and composition show great promise in regulating cell responses with potential applications in wound healing, tissue repair and regeneration, and tissue modeling