Increased work through electronic health record (EHR) messaging is frequently cited as a factor of physician burnout. However, studies to date have relied on anecdotal or self-reported measures, which limit the ability to match EHR use patterns with continuous stress patterns throughout the day. The aim of this study is to collect EHR use and physiologic stress data through unobtrusive means that provide objective and continuous measures, cluster distinct patterns of EHR inbox work, identify physicians’ daily physiologic stress patterns, and evaluate the association between EHR inbox work patterns and physician physiologic stress. Physicians were recruited from 5 medical centers. Participants (N=47) were given wrist-worn devices (Garmin Vivosmart 3) with heart rate sensors to wear for 7 days. The devices measured physiological stress throughout the day based on heart rate variability (HRV). Perceived stress was also measured with self-reports through experience sampling and a one-time survey. From the EHR system logs, the time attributed to different activities was quantified. By using a clustering algorithm, distinct inbox work patterns were identified and their associated stress measures were compared. The effects of EHR use on physician stress were examined using a generalized linear mixed effects model. Physicians spent an average of 1.08 hours doing EHR inbox work out of an average total EHR time of 3.5 hours. Patient messages accounted for most of the inbox work time (mean 37%, SD 11%). A total of 3 patterns of inbox work emerged: inbox work mostly outside work hours, inbox work mostly during work hours, and inbox work extending after hours that were mostly contiguous to work hours. Across these 3 groups, physiologic stress patterns showed 3 periods in which stress increased: in the first hour of work, early in the afternoon, and in the evening. Physicians in group 1 had the longest average stress duration during work hours (80 out of 243 min of valid HRV data; P=.02), as measured by physiological sensors. Inbox work duration, the rate of EHR window switching (moving from one screen to another), the proportion of inbox work done outside of work hours, inbox work batching, and the day of the week were each independently associated with daily stress duration (marginal R2=15%). Individual-level random effects were significant and explained most of the variation in stress (conditional R2=98%). This study is among the first to demonstrate associations between electronic inbox work and physiological stress. We identified 3 potentially modifiable factors associated with stress: EHR window switching, inbox work duration, and inbox work outside work hours. Organizations seeking to reduce physician stress may consider system-based changes to reduce EHR window switching or inbox work duration or the incorporation of inbox management time into work hours.