To investigate autonomy preferences and the factors to promote active patient participation in a primary care setting in Japan. Ninety-two hypertensive outpatients who consecutively visited a Japanese hospital between January and May of 2005 in Tokyo, Japan. This cross-sectional study was conducted by using a self-administered questionnaire. The main outcome measures were patient preferences for autonomy (i.e., decision-making and information-seeking preferences), measured by the Autonomy Preference Index (API). The variables studied were patient sociodemographic characteristics, physician characteristics based on patient preference (i.e., ability to communicate, extent of clinical experience, qualifications, educational background, gender, and age), and the Multidimensional Health Locus of Control. On the API scale from 0 to 100, the patients had an intermediate desire for decision-making (median: 51) and a greater desire for information (median: 95). A multivariate regression model indicated that decision-making preference increased when patients were woman and decreased as physician age increased, and information-seeking preference was positively associated with good communication skills, more extensive clinical experience, physicians of middle age, and patient beliefs that they were responsible for their own health, and was negatively associated with a preference for man physicians. Physicians may need to understand that patient autonomy preferences pertain to physician age and gender, physician communication ability and extent of clinical experience, and patient beliefs about self-responsibility toward health, and could use the information to promote reliable patient-physician relationships.