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Consumer-based physical activity (PA) trackers, also known as wearables, are increasingly being used in research studies as intervention or measurement tools. One of the most popular and widely used brands of PA trackers is Fitbit. Since the release of the first Fitbit in 2009, hundreds of experimental studies have used Fitbit devices to facilitate PA self-monitoring and behavior change via goal setting and feedback tools. Fitbit’s ability to capture large volumes of PA and physiological data in real time creates enormous opportunities for researchers. At the same time, however, it introduces a number of challenges (eg, technological, operational, logistical), most of which are not sufficiently described in study publications. Currently, there are no technical reports, guidelines, nor other types of publications discussing some of these challenges and offering guidance to researchers on how to best incorporate Fitbit devices in their study design and intervention to achieve their research goals. As a result, researchers are often left alone to discover and address some of these issues during the study through “trial and error.” This paper aims to address this gap. Drawing on our cumulative experience of conducting multiple studies with various Fitbit PA trackers over the years, we present and discuss various key challenges associated with the use of Fitbit PA trackers in research studies. Difficulties with the use of Fitbit PA trackers are encountered throughout the entire research process. Challenges and solutions are categorized in 4 main categories: study preparation, intervention delivery, data collection and analysis, and study closeout. Subsequently, we describe a number of empirically tested strategies used in 4 of our interventional studies involving participants from a broad range of demographic characteristics, racial/ethnic backgrounds, and literacy levels. Researchers should be prepared to address challenges and issues in a timely fashion to ensure that the Fitbit effectively assists participants and researchers in achieving research and outcome goals.