In this paper, a new method for separation, identification and quantitation of iodotyrosines and iodothyronines [3-monoiodo-L-tyrosine (MIT), 3,5-diiodo-L-tyrosine (DIT), L-thyronine (T(0)), 3,5-diiodo-L-thyronine (T(2)), 3,5,3'-triiodo-L-thyronine (T(3)) and 3,3',5,5'-tetraiodo-L-thyronine (T(4))] was described by using capillary electrophoresis with photodiode-array ultraviolet-visible detection (CE-UV). The certain influence factors were systematically investigated, including the type, concentration and pH of buffer, and additive. We found that 10mM sodium borate running buffer (pH 8.5) containing 0.10mM beta-CD as additive reagent allowed the best instrumental conditions for the optimum separation of the iodotyrosines and iodothyronines. Under optimized conditions, the analytical time was within 6 min, using an uncoated fused-silica capillary of 75 microm inner diameter with an effective length of 30 cm. The reproducibility of the migration time and peak area was less than 0.6% and 6.8%, respectively. A linear range from 10-1000 microg/mL and low limits of detection from 1.3-3.4 microg/mL were obtained at the detection wavelength of 280 nm. Our preliminary results show that the method is well suitable for determination of the hydrolysate of iodinated casein.