Johannesburg: Police are looking for the owner of the house, a woman, who was away in Johannesburg at the time of the search.
Investigations have been launched and the bodies have been sent for post mortems.
Mthatha is one of the main towns in Eastern Cape province and lies near Qunu, the final resting place of former President Nelson Mandela.
South African police said today they have discovered the frozen corpses of four newborn babies in freezers at a house in the southern city of Mthatha.
Acting on a tip-off, police raided a house on Saturday and made the grim discovery of the infants estimated to be aged between just one and two months.
"The babies were found in two freezers," police spokesman Mzukisi Fatyela told AFP.
Investigations have been launched and the bodies have been sent for post mortems.
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