In humans, physiological outputs of the body’s internal clock (i.e., saliva, serum, and temperature) can be collected to quantify the timing of the circadian system. In-lab assessment of salivary melatonin in a dimly lit environment is a common approach for adolescents and adults; however, the reliable measurement of melatonin onset in toddlers and preschoolers requires a modification of laboratory methods. For > 15 years, we have successfully collected data from ~250 in-home dim light melatonin onset (DLMO) assessments of children aged 2–5 years. Although in-home studies of circadian physiology may introduce a host of challenges and may increase the risk of incomplete data (e.g., accidental light exposure), in-home studies afford more comfort (e.g., less arousal in children) and flexibility for families. Here, we provide effective tools and strategies to assess children’s DLMO, a reliable marker of circadian timing, through a rigorous in-home protocol. We first describe our basic approach, including the study protocol, collection of actigraphy data, and strategies for training child participants to complete procedures. Next, we detail how to convert the home into a “cave”, or dim-light environment, and present guidelines for timing the salivary data collection. Lastly, we provide helpful tips to increase participants’ compliance based upon behavioral and developmental science tenets.