Capillary electrophoresis (CE) may replace many 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, hydrophobic 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 mutations 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.