Metabolomics　is　the　downstream　of　systems　biology　and　has　drawn　significant　interest　for　studying　the　metabolic　networks　from　cells　to　organisms.　To　profile　the　metabolites　in　two　different　cell　lines　(A549　and　AGS)　infected　with　influenza　A　virus,　gas　chromatography　coupled　with　mass　spectrometry　(GC/MS)　was　employed.　Some　differentiating　metabolites　in　the　cell　lines　were　tentatively　identified　using　reference　library,　interpreted　and　visualized　by　applying　principal　components　analysis　(PCA)　and　cluster　heat　map.　Consequently,　metabolic　flux　profiling　allowed　the　differentiation　of　fatty　acid　biosynthesis　and　cholesterol　metabolism　during　viral　replication　in　the　cell　lines.　The　change　in　fatty　acid　turnover　was　also　observed.　Metabolomics　investigation　also　revealed　the　different　responses　between　A549　and　AGS　cell　lines　to　the　virus　infection.　From　the　pattern　recognition　results,　AGS　cell　line　might　be　more　susceptible　to　influenza　A　virus.　Regarding　the　fact　that　AGS　is　a　poorly　differentiated　gastric　adenocarcinoma　cell　line　whereas　A549　is　a　relatively　differentiated　lung　tumor　one,　it　is　speculated　that　viral　replication　might　be　associated　with　the　cell　differentiations.　©　2010　Elsevier　B.V.