Silica and silica-based nanoparticles have been widely used for therapeutic and diagnostic applications in cancer mainly through delivery of drugs, genes and contrast agents. Development of synthesis methods has provided the possibility of fabricating silica nanoparticles with different sizes in nanometer ranges as well as silica-based multimodal nanoparticles with many innovative properties and intriguing applications in biomedicine. The surface of silica particles facilitates different methods of surface modifications and allows conjugation of various biomolecules such as proteins and nucleic acids. In this review, different methods of fabrication of silica and silica-based nanoparticles, their surface modification and the application of these nanoparticles in molecular imaging are discussed. Overall, the aim of this review is to address the development of silica and silica-based multifunctional nanoparticles that are introduced mainly for molecular imaging applications using optical, magnetic (MRI), X-ray (computed tomography) and multimodal imaging techniques.