Two published procedures for glass capillary column production are applied to produce capillaries for chromatography of polar natural compounds. Soda lime glass capillaries, after leaching with aqueous HCL, are either treated with colloidal silicic acid or with barium carbonate and coated with either Silar 7CP or SE 52. A test mixture as well as polar carbohydrate and peptide mixtures are chromatographed on the different columns and their chromatographic properties are evaluated. Combined capillary gas chromatography-electron impact and chemical ionization mass spectrometry are used for identification of the peptide sequence.