Introduction: An evolution in bioanalytical methodologies to identify and quantify drug metabolites has led to a wealth of biotransformation information during preclinical and early clinical testing phases. However, this abundance of metabolism data has not clarified how to select the most important circulating human metabolites for safety assessment. Consequently, more stringent regulatory expectations for a comprehensive approach to human metabolism have led pharmaceutical sponsors to employ a variety of novel methods to estimate circulating drug metabolites in humans and animals. Areas covered: This review provides context for 'why' human circulating metabolites must be qualified for safety in animals. A detailed overview is also presented concerning 'where,' 'how' and 'when' to conduct these assessments during drug development. Expert opinion: A human metabolite qualification strategy is now a required element of the drug safety package submitted with a new drug application (NDA). The important question is whether or not this additional information, about metabolite safety, is making human drugs any safer. Currently, this is a debatable issue, especially because stand-alone metabolite testing is fraught with its own challenges. As drug development moves into the twenty-first century, there is a pressing need for more sophisticated methodologies to address human drug and metabolite safety.