The powerful Syntsha union of medical workers which called the protest said hospitals had ground to a halt.
Syntsha secretary general Pissyamba Ouedraogo told AFP that the protest was aimed at "making the government see reason."
"There is no doubt that health services throughout the country are blocked as the personnel have not showed up," Ouedraogo said.
Health Minister Smaila Ouedraogo claimed that there were just four sticking points out of the original 63 demands made by the unions and added he was hopeful they would be resolved soon.
Patients were left to fend for themselves at the Yalgado Ouedraogo university hospital, the largest in the country, an AFP correspondent said.
There was only one doctor in the emergency ward.
A doctor at another medical facility in the capital Ouagadougou said he had turned up as it was "a matter of conscience."
"This strike is not normal and it is not fair," he said. "When the sick are struggling to buy medicines because they have no money, they are demanding higher salaries," said Bernard Kabore, whose brother needs a second operation after an accident.
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