One of the main challenges in food contact materials research is to prove that the presence of non-intentionally added substances (NIAS) is not a safety issue. Migration extracts may contain many unknown substances present at low concentrations. It is difficult and time-consuming to identify all these potential NIAS and concurrently to assess their health risk upon exposure, whereas the health relevance at low exposure levels might not even be an issue. This paper describes a scientifically based, but pragmatic safety assessment approach for unknown substances present at low exposure levels in food contact matrices. This complex mixture safety assessment strategy (CoMSAS) enables one to distinguish toxicologically relevant from toxicologically less relevant substances, when related to their respective levels of exposure, and allows one to focus on the substances of potential health concern. In particular, substances for which exposure will be below certain thresholds may be considered not of health relevance in case specific classes of substances are excluded. This can reduce the amount of work needed for identification, characterisation and evaluation of unknown substances at low concentration. The CoMSAS approach is presented in this paper using a safety assessment of unknown NIAS that may migrate from three carton samples.