To clarify the mechanism underlying the inactivation of Escherichia coli (E. coli) cells subjected to atmosphericpressure argon (Ar) plasma jet irradiation, we focused on phospholipids, the main components of the cell wall and membrane of E. coli. Commercially available standard samples of phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) were irradiated with an atmospheric-pressure Ar plasma jet in air for 5 s. The phospholipids irradiated with the plasma jet were separated by thin-layer chromatography (TLC), and the results showed that PE was unchanged even after plasma jet irradiation, whereas PG was degraded into several substances. One of them was identified as lysophosphatidylglycerol (LPG), a lysophospholipid of PG, by liquid chromatography-mass spectrometry (LC-MS). From these results, we inferred that PG in the cell wall and membrane was degraded into LPG and a fatty acid by plasma jet irradiation, and that the cell wall and membrane were disrupted, inactivating E. coli.