Clinical uncertainty is a source of variation in medical decision-making as well as a source of work-related stress. Increasing enrollment in organized health care systems has intensified interest in understanding referral utilization as well as issues such as physician dissatisfaction and burnout. We examined whether primary care physicians' affective reactions to uncertainty and their job characteristics were associated with use of referrals and burnout. Data came from mail surveys of primary care physicians practicing in two large group model health maintenance organizations (HMOs) in the USA. Consistent with past research, we found that younger physicians had higher referral rates than older physicians, and that general internists had higher rates than either family practitioners or pediatricians. Greater stress from uncertainty increased referrals and referrals were negatively correlated with heavier work demands (patient visits per hour). Greater stress from uncertainty, perceived workload (too high) and a sense of loss of control over the practice environment were associated with higher levels of burnout.