A review of the challenges to the scientific basis of firearms and tool mark identification in recent court cases have common themes. These include questions about whether tool manufacture results in sufficient individuality to distinguish one among many of the same tool type and the related issue of subclass characteristics. Other challenges relate to the change in tool surfaces over time, which affects time-related matching of a tool to a tool mark. Other challenges relate to the lack of objective criteria, the need for statistics and databases, the lack of adequate validation of tool identification, and inadequate proficiency testing. These challenges have mostly been published in journals that offer legal arguments rather than scientific research. Scientific articles on the challenges have been review articles. In addressing the challenges posed, this article draws on a comprehensive review of the available literature to show that firearms and tool mark identification is rooted in firm scientific foundations. The discipline is based in the precepts of the scientific method as expressed in the Theory of Identification developed by the Association of Firearms and Toolmark examiners. Further, if taken into account in a particular case, issues of differing identification criteria, subclass characteristics, and changes in a tool's surface over time do not invalidate the scientific basis for the testimony of experts in the firearms and tool mark discipline. Proficiency tests and error rates have been studied and can provide courts with a useful guide to the frequency with which misidentifications occur based on appropriate scientific methods and controls. 65 references