Silk is a widely accepted biomaterial for tissue regeneration owing to its tunable biomechanical properties and ease of chemical modification. However, a number of aspects associated with its clinical use are still debated. Indeed, to achieve clinical success, a biomaterial must favorably interact with host tissues without evoking local or systemic immuno-inflammatory responses. The analysis of immune responses associated with silk under in vitro and in vivo conditions provides useful insights, improving the understanding of the functional characteristics of silk biomaterials and further promoting their clinical application. Silk evokes moderate immune responses upon implantation in vivo, depending on the material structure, fabrication method, degradation time, and implantation in soft or hard tissue sites, which rapidly subside within a few days/weeks. In vitro studies indicate that its immune-stimulatory properties are largely due to inherent protein conformation and differential processing parameters. Strategically controlled levels of immune responses in vivo with marginal immunogenicity of silk-based biomaterials may contribute to matrix remodeling and replacement by native tissue matrix around the implanted site. Therefore, immunomodulatory strategies should be developed to promote the use of silk-based biomaterials as promising candidates for numerous clinical applications.