This study was purposed to investigate the diagnostic value of fluorescence in situ hybridization (FISH) technique for the childhood acute myeloid leukemia (AML). The medical data of 179 children with AML (aged ≤ 16 years) were retrospectively studied, who were initially diagnosed in our hospital from April 2005 to April 2010. Through the analysis of the results of FISH, chromosome banding analysis and polymerase chain reaction, the difference and complementarity between FISH and other 2 methods for detecting the fusion genes were explored. The results indicated that the detection rate of genetic abnormality with FISH was higher. The PML/RARα probe was used in 27 AML-M3 patients, 22 out of whom were evaluated as PML/RARα positive. The AML1/ETO probe was used in 24 AML-M2b patients and all of them were evaluated as AML1/ETO positive. The CBFβ/MYH11 probe was used in 4 AML-M4Eo patients and all of them were evaluated as CBFβ/MYH11 positive. It is concluded that FISH is a sensitive method for detecting fusion genes and the results of FISH have a good correlation with the chromosome banding analysis and polymerase chain reaction. The combination of FISH with other 2 methods improves the detection rate of genetic abnormality, which is useful for the diagnosis and typing of childhood AML.