Silicone elastomers have the potential to be a valuable biomaterial due to their mechanical and chemical properties, easy processing, and high gas permeability. Some inherent properties of the pure silicone implant such as high hydrophobicity and low load bearing capacity can be problematic for biomedical applications. The issues were addressed by fabricating hydroxyapatite nanofiber/polydimethylsiloxane nanocomposites. The morphology of nanocomposite structures was visualized by high resolution transmission electron microscopy and field emission scanning electron microscopy. Improved mechanical strength and compliance of the prepared nanocomposite structures were obtained by frequency sweep and creep measurements. Surface hydrophilicity of polydimethylsiloxane was enhanced by hydroxyapatite nanofiber incorporation into the polymer matrix. The cytotoxicity and biocompatibility of the structures were analyzed using breast epithelial cells (MDA MB 231 cell line). These studies showed that the nanocomposite scaffold did not leach any cytotoxic material and showed better cell adhesion and cell proliferation compared to the unfilled elastomer.