Objective To investigate applied value of automated nucleic acid purification system in clinical detection by real-time fluorescence quantitative PCR. Methods HCV and enteroviruses nucleic acid samples were extracted by nucleic acid extraction apparatus and hand-made method,respectively. The extracted products were detected by fluorescent quantitative PCR. Results The extraction efficiency of automated nucleic acid purification system showed no significant difference between two different magnetic kits(t1=-0.805,P1=005;t4=-1.952,P40.05)The extraction efficiency of automated nucleic acid purification system obviously better than manual method(t=-3.314,P0.01;t=--3.576,P0.01),the extraction efficiency of two different magnetic kits is consistent. extraction of 30 samples used about 2h by manual method. extraction of32 samples used about 1h by automated nucleic acid purification system. Conclusions The extraction efficiency of automated nucleic acid purification system obviously better than hand-made method.NP968 automated nucleic acid purification system is open for different magnetic beads kits. automated nucleic acid purification system is quick,efficient and sample method for extraction and worthy for laboratory applciation.