Chitosan/silk fibroin multilayer thin films were assembled using layer-by-layer deposition. The resultant multilayer Films contained nanofibers aligned parallel to the dipping direction. Fiber deposition and orientation was enabled uniquely by a judicious choice of solvent and drying conditions and layer-by-layer assembly with chitosan. The deposition of oriented nanotibers was found to be the result of a unique combination of layer-by-layer and Langmuir-Blodgett type processing. Fiber orientation was confirmed by fast Fourier transform (FFT) analysis of optical micrographs and atomic force microscopy (AFM). Bidirectional fiber alignment was realized by rotating the substrate between multilayer deposition steps. Infrared spectroscopy revealed that the silk fibroin adopted the silk II secondary structure in the deposited films. We anticipate that these anisotropic films are able to combine the biocompatibility of a natural polymer system with the mechanical strength or SF, two properties useful in many biological applications including scaffolds suitable for guiding cell attachment and spreading.