When a sample is found to be positive during routine GM tobacco (GMT) testing, a PCR analysis for other specific genes used in GM tobacco, such as TMV-CP, CMV-CP, Bt-cryIA(C), will usually be carried out. Often it is not possible to distinguish between different transgene events in cured tobacco leaf samples containing the same gene of interest, when the only difference is the point of insertion into the tobacco genomic DNA. However, if this region could be characterised it could be used to distinguish different transgene insertion events and provide a means of tracking the origin and dissemination of each GMT event. This report describes the analysis of several GM tobacco samples developed for research purposes and the methods used. A PCR walking method was used to characterise the DNA between the known segment of the T-DNA and the unknown region of the plant genome. After defining this junction region, specific primers can be designed for routine and rapid identification of different transgene events.