Acute kidney injury is associated with significant morbidity and mortality in hospitalized patients. Clinical trials for acute kidney injury have been hampered not only by a paucity of appropriate potential therapeutic agents, but also by several clinical trial design challenges. First, for novel therapies to have the best chance at efficacy, early patient identification is critical. Second, for certain novel therapies with a mechanism of action directed at the underlying disease state (e.g., sepsis) or a specific pathogenic process, careful disease phenotyping may be required. Third, even among patients with AKI, risk stratification may be required to select a higher-risk subset for clinical trials. Finally, clinical endpoints for clinical trials must be considered carefully, as patients may die for reasons unrelated to AKI, including withdrawal of support. However, these challenges are not unique to AKI; some possible solutions including alternative endpoints used in other clinical trial settings are reviewed here.