Capillary electrophoresis (CE) may replace man, conventional clinical laboratory methods, such, as electrophoresis. Southern blotting, sequencing and HPLC (High-performance liquid chromatography). It is an ideal technique due to analytical speed, the possibility of handling great amount of samples, its capacity to separate small molecules according to their size, charge, hydrophobicity and stereo-specificity, its good reproducibility, The use of small amounts of sample and reagents, its low costs and easy handling. The diagnosis of hereditary diseases or the predisposition to polygenic diseases related to specific initiations or polymorphisms, can be carried out with this method. In clinical laboratories, this technique is being used for the analysis of several substrates Present in urine or serum and for the diagnosis of some infectious agents. It is also a firsthand tool in forensic medicine for human identification and anthropology (Rev Med Chile 2009; 137: 946-56).