Traditional forensic chemical comparisons of polymeric materials are often affected by fingerprinting agents that enhance and visualise finger-marks. This can inhibit detailed analysis used to provide an association or discrimination between two samples. In this study, we have demonstrated that the method for polymer comparisons using isotope ratio mass spectrometry analysis is not affected by fingerprinting matter on the surface in contrast to other forensic instrumental tests. A selection of resealable bags was analysed for carbon and hydrogen isotope ratio values of bags that had been subject to various fingerprinting agents and compared to values of untreated bags. The results showed no significant difference between samples that had been fingerprinted from those that were untreated.