Japan is an advanced country with high standards of hygiene and few endemic diseases. There are no special immunisations needed to visit Japan and, other than bringing prescription medications from home, no special preparations need to be made.
Medical care in Japan is reasonably priced, particularly in comparison to costs in the USA. The quality of care varies enormously, from completely competent to dangerously incompetent. You’ll usually find the best doctors in large teaching hospitals, like Kyoto University Hospital. Small local clinics should be avoided unless there are no other choices.
Many hospitals and clinics will be wary of treating foreigners because they don’t know how payment will be made (most Japanese belong to the national health system). Where necessary, show proof of your travel insurance or cash. If treatment is absolutely necessary, demanding firmly but politely to be treated is the best approach.
Kyoto University Hospital is the best hospital in Kyoto. There is an information counter near the entrance on the ground floor that can point you in the right direction. Patients without appointments are seen in the morning. Go at 8.30am to reduce your wait (they start seeing patients at 9am).
Tap water is safe to drink.