Encapsulation, specifically microencapsulation is an old technology with increasing applications in pharmaceutical, agrochemical, environmental, food, and cosmetic spaces. In the past two decades, the advancements in the field of nanotechnology opened the door for applying the encapsulation technology at the nanoscale level. Nanoencapsulation is highly utilized in designing effective drug delivery systems (DDSs) due to the fact that delivery of the encapsulated therapeutic/diagnostic agents to various sites in the human body depends on the size of the nanoparticles. Compared to microencapsulation, nanoencapsulation has superior performance which can improve bioavailability, increase drug solubility, delay or control drug release and enhance active/passive targeting of bioactive agents to the sites of action. Encapsulation, either micro- or nanoencapsulation is employed for the conventional pharmaceuticals, biopharmaceuticals, biologics, or bioactive drugs from natural sources as well as for diagnostics such as biomarkers. The outcome of any encapsulation process depends on the technique employed and the encapsulating material. This chapter discusses in details (1) various physical, mechanical, thermal, chemical, and physicochemical encapsulation techniques, (2) types and classifications of natural polymers (polysaccharides, proteins, and lipids) as safer, biocompatible and biodegradable encapsulating materials, and (3) the recent advances in using lipids for therapeutic and diagnostic applications. Polysaccharides and proteins are covered in the second part of this chapter.