Described is a capillary column cartridge. The cartridge can be used to perform separations according to various techniques such as capillary gas chromatography, capillary electrophoresis and capillary liquid chromatography. The cartridge includes a capillary column secured in a cartridge body. The capillary column includes an inlet port and an outlet port that, in some embodiments, are disposed on a planar surface of the body. When the body is engaged to a separation system module, the inlet port is aligned to receive a sample to be separated and the outlet port is aligned to provide the separated sample to the separation system module. The path of the capillary through the body has a non-planar path shape such as a coil shape. Consequently, longer column lengths can be accommodated, leading to an improvement in separation resolution. The body can include a material having a high thermal conductivity to achieve improved thermal performance.