The endogenous and exogenous urinary metabolites of rats passively exposed to sidestream cigarette smoke (SCS) were analysed to study the changes of urinary metabolites with a metabonomics method. The contents of total urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), total 1-hydroxypyrene (1-HOP) and 3-hydroxybenzo[a]pyrene (3-HOBaP) in urine sampled from rats of three groups, a control group, a group treated with blended reference cigarettes (non-menthol) and a group treated with menthol cigarettes, were determined to assess the toxins of exposure to SCS. The total NNAL level was determined by LC-ESI-MS/MS and the levels of 1-HOP and 3-HOBaP were determined by ultra performance liquid chromatography (UPLC) with fluorescence detection (FLD). The urinary endogenous metabolites of all samples were analysed with UFLC / IT-TOF-MS, the data were processed with chemometrics, and the effects of exposure time were evaluated. Eleven endogenous metabolites related to smoke exposure were identified, their contents were compared, and the results showed that SCS had complex effects on rats. The contents of total NNAL and 3-HOBaP in samples from the menthol cigarette group were statistically significantly lower than those from the non-menthol cigarette group (P <0.01 and P <0.05, respectively), whereas 1-HOP content was statistically unchanged (P >0.05). The sidestream smoke of menthol and non-menthol cigarettes influenced methyl-hippuric acid, glucuronate, and pantothenic acid greatly, however xanthurenic acid was not affected. The contents of kynurenic acid and N2-succinyl-L-ornithine in urine of rats passively exposed to sidestream smoke of non-menthol cigarettes decreased, while suberylglycine content in that of menthol cigarettes increased significantly. Menthol in cigarettes had positive and negative effects on the amino acid metabolisation in rats. In general, the urinary metabolic profiling of the menthol cigarette group was closer to that of the control group.