Over the last few years, research on silica nanoparticles has rapidly increased. Particularly on mesoporous silica nanoparticles (MSNs), as nanocarriers for the treatment of various diseases because of their physicochemical properties and biocompatibility. The use of MSNs combined with therapeutic agents can provide better encapsulation and effective delivery. MSNs as nanocarriers might also be a promising tool to lower the therapeutic dosage levels and thereby to reduce undesired side effects. Researchers have explored several routes to conjugate both imaging and therapeutic agents onto MSNs, thus expanding their potential as theranostic platforms, in order to allow for the early diagnosis and treatment of diseases. This review introduces a general overview of recent advances in the field of silica nanoparticles. In particular, the review tackles the fundamental aspects of silicate materials, including a historical presentation to new silicates and then focusing on the key parameters that govern the tailored synthesis of functional MSNs. Finally, the biomedical applications of MSNs are briefly revised, along with their biocompatibility, biodistribution and degradation. This review aims to provide the reader with the tools for a rational design of biocompatible MSNs for their application in the biomedical field. Particular attention is paid to the role that the synthesis conditions have on the physicochemical properties of the resulting MSNs, which, in turn, will determine their pharmacological behavior. Several recent examples are highlighted to stress the potential that MSNs hold as drug delivery systems, for biomedical imaging, as vaccine adjuvants and as theragnostic agents.