A chromatography column for microwave heating either incorporates microwave absorbing material into the column itself or positions the column adjacent to microwave absorbing material so that the column and the chromatography sample contained therein are heated by the microwave absorbing material via conduction or convection. For example, a microwave absorbing material (e.g., ferrite) can be fused into the inner silica layer or incorporated in an outer polymer layer of the column. Microwave absorbing material can also be incorporated into an external element (e.g., an outer tube, sleeve, or spool) positioned adjacent to the chromatography column. A layer of thermal insulation can be placed around the column to decrease the rate of heat loss. Optionally, a gap can be provided between the chromatography column and thermal insulation to further reduce heat loss during the heating cycle and to accelerate cooling at the end of the heating cycle by making it possible to ventilate the heated column. The chromatography column assembly can be protected from overheating by selecting a microwave absorbing material having a loss factor that decreases rapidly above a predetermined maximum temperature.