High-throughput and high-content screening enables large scale, cost-effective experiments in which cell cultures are exposed to a wide spectrum of drugs. The resulting multivariate data sets have a large but shallow hierarchical structure. The deepest level of this structure describes cells in terms of numeric features that are derived from image data. The subsequent level describes enveloping cell cultures in terms of imposed experiment conditions (exposure to drugs). We present Screenit, a visual analysis approach designed in close collaboration with screening experts. Screenit enables the navigation and analysis of multivariate data at multiple hierarchy levels and at multiple levels of detail. Screenit integrates the interactive modeling of cell physical states (phenotypes) and the effects of drugs on cell cultures. In addition, quality control is enabled via the detection of anomalies that indicate low-quality data, while providing an interface that is designed to match workflows of screening experts. We demonstrate analyses for a real-world data set, CellMorph, with 6 million cells across 20,000 cell cultures.