The reproducibility of high-throughput cell-based assays is dependent on having a consistent source of cells for each experiment. Developing an understanding of the nature of cells growing in vitro and factors that influence their responsiveness to test compounds will contribute to the development of reproducible cell-based assays. Using good cell culture practices and establishing standard operating procedures (SOPs) for handling cultures can eliminate several potential contributors to variability in the responsiveness and performance of cells. The SOPs for handling each cell type must have clear and detailed instructions that can be understood and followed among different laboratories. The SOPs should include documenting the source of cells and authenticating their identity, both of which have become required to achieve peer acceptance of experimental data. Variability caused by biological issues such as phenotypic drift can be reduced by using standardized subculture procedures or using cryopreserved cells to set up experiments. Variability caused by inconsistent dispensing of cells per well and edge effects can be identified by measuring how many cells are present and whether they are alive or dead. Multiplex methods for real-time measurement of viable or dead cell number in each sample can be used for normalizing data and determining if proliferation or cytotoxicity has occurred during the experiment. Following good cell culture practices will go a long way toward executing reproducible cell-based assays. Resources will be included describing good cell culture practices, cell line authentication, and multiplex determination of cell number as an internal control.