Background Second opinion (SO) is widely recognized in Japan, but we do not know how patients view and use SO. Objectives To investigate optimum seeking of SO in Japan's universal health‐care system. Design, participants, and methods Survey of patients at Tokyo Medical and Dental University Hospital. Of 365 responses, 67 had experienced SO with standardized protocol at SO Clinic; 82 had obtained SO elsewhere without instruction; 216 had never sought SO. Main outcome measures Views of values and risks of SO. Results Second opinion patients with standardized protocol better understood their illness, treatment options, individualized plan, and uncertainty in medicine, and also reported improved decision making compared with SO patients without the protocol (P < 0.05). However, more than half of respondents misunderstood SO as a way to change doctors or treatment. Second opinion respondents (n = 149) had a propensity to request treatment changes (P < 0.1) and more than one‐third (n = 82) did not tell SO doctor they were being treated by another doctor. The absolute majority of non‐SO patients would seek SO for a serious illness but would hesitate to tell their doctors. Discussion and conclusion Respondents recognized value of SO to improve understanding and decision making. This study also found risks in SO misuse which may be reinforced by Japan's cultural tendencies and universal health‐care system. Our findings suggest steps to increase the benefit of SO: ensure involvement of original doctor, instruct patients about SO and help them organize their thinking before SO and facilitate patients' return to the treating doctor for discussion and decision making.