Abstract: GC-MS was applied to the determination of malondialdehyde (MDA) in plasma and liver homogenate of rat. The sample was reacted with 1.0 mol·L-1 NaOH at 60 ℃ for 60 min to produce MDA, which was derivatized with pentafluorophenyl hydrazine (PFPH). The derivatized product obtained was separated on HP-5MS chromatrographic column, and determined by MS with selected ion monitoring mode and electron impact ionization source. Ions of m/z 234 and 248 were selected for the quantitative analysis of MDA-PFPH and the internal standard Me-MDA-PFPH respectively. Linearity ranges of malondialdehyde were kept from 1.0 to 50.0 μmol·L-1 (in plasma) and 50 to 500 μmol·L-1 (in liver homogenate), with recovery in the ranges of 94.6%-103% (in plasma) and 93.2%-106% (in liver homogenate). Values of intraday and interday RSD′s (n=6) found were all less than 5%.