The use of capillary electrophoresis (CE) for the separation of peptides specific to type I and type II collagen is evaluated. The aim of this work is to develop a method to characterize cartilage, cartilage repair tissue, and tissue engineered cartilage. The analysis is dependent on the cleavage of collagen into constituent peptides by cyanogen bromide. A number of these peptides are specific to the collagen type. CE is evaluated for the separation of these specific peptides using uncoated and coated capillaries over a wide range of pH and buffer concentrations. Separation of peptides specific to type I and type II collagen is achieved using a Supelco CElect N capillary and a 100mM phosphate buffer at pH 6. Meniscal cartilage is characterized using this method. The proportion of type I collagen to type II collagen corresponds well with that reported by others and indicates the potential of this method for the characterization of cartilage.