Endogenous aliphatic and acetylated polyamines (PAs) are known as essential components to regulate about metabolic functions. Imbalance of polyamine metabolism may be bringing about the several pathological processes. In this study, a new sample preparation method and multiple reaction monitoring (MRM) mode for simultaneous measurement of four aliphatic and five acetylated PAs in plasma and lung tissue samples was developed by liquid chromatography–tandem mass spectrometry (LC−MS/MS). Characteristic ions in MRM mode with electrospray ionization (ESI) permitted the accurate and selective analysis of PAs. In the optimal conditions, this method showed good linearity (r ≥ 0.9970) for the range of 0.5–10 ng with limit of detection (LOD) of 0.003–0.8 pmol and limit of quantification (LOQ) of 0.01–2.6 pmol. The repeatabilities of intra and inter days as a percentage of relative standard deviation (% RSD) varied from 0.4–15.4 (% RSD). And accuracy as a percentage of relative error (% RE) was from -17.3–16.2 (% RE). When applied to the analysis of PAs in plasma and lung tissue samples from control and asthma mice, nine PAs were positively identified and determined by LC−MS/MS. The percentage composition of putrescine and spermidine in plasma as major PAs ranged from 20.33 ± 4.51–22.13 ± 2.37 and 67.85 ± 2.84–69.59 ± 5.98, respectively. While, percentage composition of spermidine and spermine as major PAs in lung tissue ranged from 27.61 ± 1.71–28.74 ± 5.91 and 67.60 ± 5.99–69.25 ± 2.08, respectively. In the asthma group compared to control group, level of N1-acetylspermine (p<0.03) was significantly reduced in plasma, while level of putrescine (p<0.02) was significantly increased in lung tissue. The percentage composition of each PA from asthma group was normalized to the corresponding mean value of control group, which were used for creating star pattern graph. The distorted star graphic pattern of the asthma group was different from nonagonal shape of the control group. Therefore, the present PA profiling method by LC−MS/MS will be useful for the biochemical monitoring of various disease state including asthma.