The field of cell-based screening is expanding rapidly as innovations in target selection and instrumentation increase the number of targets that can be efficiently screened in cellular formats. Cell-based screens can be configured to provide a broad range of data on chemical compound activity, mechanism of action and drugability. However, the decision to pursue a cell-based approach should not be made lightly, as cell-based assays can be challenging to implement in the high-throughput screening (HTS) laboratory. In this review, we describe three case studies in which targets were successfully interrogated in cell-based HTS, and highlight the necessary steps to ensure the validity of these screens.