During quality control of doxofylline, a novel impurity was detected, which was above the identification threshold defined by ICH. First, a liquid chromatographic method compatible with mass spectrometric (MS) detection was developed. Based on tandem multistage MS and high resolution MS data, the unknown impurity was found to consist of two theophylline groups connected by a methylene group. The structure was further confirmed by 1D and 2D nuclear magnetic resonance (NMR) experiments after semi-preparative isolation. In addition, the formation of the impurity was also discussed.