Environmental factors and exposures may contribute to many serious diseases afflicting humans. Biomarkers are useful to understand disease processes and identify early events leading to disease. The National Toxicology Program (NTP) convened a workshop in September 2006 to help identify biomarkers that could be used in toxicology studies with rodents to predict disease outcome and detect early events in disease processes. Expert scientists reviewed biomarkers for disease/injury related to the heart, lung, and/or changes in lipid/carbohydrate metabolism and made recommendations for those that could be incorporated into NTP studies on a routine or selective basis. Although numerous biomarkers were discussed, only a few were considered amenable for routine use. This article summarizes recommendations for the most promising biomarkers and presents the NTP perspective on those that will be included in the bioassay program on a routine or special study basis. Breakout group reports and additional information on the workshop, including participants, presentations, and background materials, are posted on the NTP Web site http://ntp.niehs.nih.gov/go/20940.