Aim: We investigated the effect of mainstream cigarette smoke (CS) exposure and a protocol of discontinuation of smoke exposure mimicking smoking cessation on liver lipid and transcriptome profile in the ApoE-/- mouse, a well-established model for human atherogenesis. Methods: Livers obtained from ApoE-/- mice exposed to either (i) mainstream smoke of the 3R4F reference research cigarette for six months (CS), (ii) fresh air for six months (sham), or (iii) CS for 3 months followed by fresh air for 3 months (cessation), were extracted for lipids using a robotic-assisted method and analyzed on six different mass spectrometric platforms. Targeted and non-targeted mass spectrometry methods allowed quantification of more than 200 lipid species. In addition, the liver transcriptome was profiled on Affymetrix GeneTitan:GeneChip® HT mg-430 PM plates. Results: In liver, exposure to cigarette smoke elevated several lipid species including free and esterified cholesterol, triacylglycerols, phospholipids, sphingomyelins, and ceramides. The concentration of triacylglycerols further increased upon smoke exposure cessation, correlating with the increase of body weight, whereas the concentration of phosphatidylglycerols and sphingomyelins was reduced. Gene set enrichment analysis of the transcriptomes between the 3 conditions revealed biological functions that are regulated by CS exposure in the liver of ApoE-/- mice: glutathione metabolism (detoxification), oxidoreduction (energy), coenzyme biosynthesis, phosphorus metabolic process and lipid biosynthesis. The enrichment of these gene sets was clearly reduced in the cessation setup. Conclusions: Coupled investigation of detailed lipidomics and transcriptomics profiles, taking into account co-factors such as total body weight and body weight progression in the weeks before profiling, enabled to highlight, in a mouse model of atherogenesis, lipid species which are differentially regulated by cigarette smoke exposure and upon smoking cessation.