One of the key areas of importance in biotechnology and bioengineering is molecular complexation (MC). MC is useful in selectivity, separation, and solubilization of biomolecules. While many complex, natural MC agents exist, such as proteins and antibodies, relatively few engineered MC materials are available. Inorganic, insoluble MC agents, such as zeolites, are widely used in petroleum catalysis. Carbon Buckminster fullerenes ("bucky balls") can complex small neutral molecules, but are relatively insoluble and difficult to manufacture. Crown ethers have been used for molecular complexation, but are costly to synthesize and have limited capacities. One class of highly useful MC agents are cyclodextrins (CDs). These naturally-occurring, water-soluble cyclic glucans are used in a variety of food, pharmaceutical, and analytical applications. Due to the availability of multiple reactive hydroxyl groups, the functionality of CDs can be greatly increased through chemical modification. A host of new applications are being explored, including enzyme mimicry, molecular recognition, chromatographic separation, and solubilization. This review describes recent applications of modified cyclodextrins in bioprocessing and medicine.