Transgenic papaya (Carica papaya L.) was produced with the introduction of replicase (rep) gene for resistance to papaya ringspot virus (PRSV). In order to investigate the potential unintended compositional changes in transgenic papaya, profiles of volatile organic compounds (VOCs), sugar/polyals, organic acids, carotenoids and alkaloids in transgenic and non-transgenic papaya were obtained respectively by HPLC, GC–MS and LC–MS, and compared mutually by multivariate statistical methods, including principal component analysis (PCA) and similarity analysis method. Results showed that the composition in transgenic papayas exhibited great similarity to non-transgenic counterparts for measured components. The contents of important nutrients of &amp;#946;-carotene and vitamin C and two natural toxicants, including benzyl isothiocyanate (BITC) and carpaine, were compared by analysis of variance (ANOVA). The results also showed that content was similar between transgenic papayas and non-transgenic counterparts for these components. The variation of composition in papaya caused by genetic effect was slight during two harvesting times during our work. It is hoped that this study could provide some reference value for a safety evaluation of transgenic papaya from the compositional point of view, and could also propose a method for discrimination of transgenic food from non-transgenic counterparts.