The doctors called the strike at 8 am as the week began in an effort to pressure employers to provide better compensation in an ongoing labour dispute.
Patients with emergencies will still receive care, but scheduled surgeries will be moved to another day.
“According to reports from our state associations about 200 community hospitals are affected nationwide – but with differing intensity in each state,” said Hans-Jörg Freese, spokesperson for the Marburger Bund doctor's union.
The states of Bavaria, Baden-Württemberg, North Rhine-Westphalia and Rhineland-Palatinate will likely be the hardest hit, he added. Doctors will not strike in Hamburg or Berlin, where they have already reached new wage agreements with local employers.
Doctors are expected to gather for a demonstration in Munich at 3 pm.
The wage talks on behalf of some 55,000 doctors in more than 700 communities collapsed in April, and 93 percent of the Marburger Bund members voted to strike.
The union is demanding a five percent pay raise and better on-call duty compensation.
While state clinics say German doctors are already among Europe's top earners, physicians complain they are overworked and underpaid.