Genomic biomarkers play an increasing role in both preclinical and clinical application. Development of genomic biomarkers with microarrays is an area of intensive investigation. However, despite sustained and continuing effort, developing microarray-based predictive models (i.e., genomics biomarkers) capable of reliable prediction for an observed or measured outcome (i.e., endpoint) of unknown samples in preclinical and clinical practice remains a considerable challenge. No straightforward guidelines exist for selecting a single model that will perform best when presented with unknown samples. In the second phase of the MicroArray Quality Control (MAQC-II) project, 36 analysis teams produced a large number of models for 13 preclinical and clinical endpoints. Before external validation was performed, each team nominated one model per endpoint (referred to here as nominated models) from which MAQC-II experts selected 13 candidate models to represent the best model for each endpoint. Both the nominated and candidate models from MAQC-II provide benchmarks to assess other methodologies for developing microarray-based predictive models.