Salivary cortisol has emerged in pediatric research as an easy-to-collect, relatively inexpensive, biologic marker of stress. Cortisol is highly variable and is responsive to a wide range of factors that should be considered when incorporating this measure into research with children. Strategies for sample collection include: (1) standardizing the time for sample collection, including baseline samples; (2) using consistent collection materials and methods; (3) controlling for certain drinks, foods, medications, and diagnoses; and (4) establishing procedures and protocols. Other strategies for laboratory analyses include: (1) selecting the appropriate assay and laboratory; (2) identifying units of measure and norms; and (3) establishing quality controls. These strategies control extraneous variables and produce reliable and valid salivary cortisol results.