Polymerase chain reaction (PCR) is a key procedure in modern molecular biology but may be adversely affected by many factors and it is difficult to optimize reaction conditions; a technically simple and effective method to set up an optimal PCR-amplified system is required. Uniform design (UD) is a method that enables many factors to be investigated. For example, the dhaT gene from Klebsiella pneumoniae was amplified and the optimization of the amplified parameters including concentration of Mg2+, annealing temperature, annealing time and number of cycles based on UD was reported. After only 12 experimental trials, an optimal PCR-amplified result was obtained, demonstrating the value of UD for optimization of PCR. (C) 2004 Society of Chemical Industry.