At least one person was injured in the attacks.
Santander and Gijon, some 130km (80 miles) apart on Spain's northern coast, are packed with holidaymakers at this time of year and the explosions appeared to fit into ETA's strategy of seeking to undermine Spain's key tourism industry.
A small bomb exploded in one of Santander's busiest streets, close to a major office of Spain's biggest bank, Santander Central Hispano (SCH), and near regional government offices.
The bomb caused no injuries and only minor damage, officials said.
Almost simultaneously, another explosion occurred near a restaurant in Gijon, officials said.
It was not immediately confirmed that it was a bomb, but a police spokesman said one person had been injured.
The Santander bomb had been left in a bag, according to reports.
Police were searching the city for more bombs, a regional government spokesman said. "All of the centre ... is cordoned off," he said. "We are in high season. An event of this kind does not help tourism," he added.
A spokesman for the Basque regional police said a caller to Basque newspaper Gara had earlier warned that ETA had planted two bombs.
Officials said the Santander device appeared to be similar to two bombs that exploded in Spanish resorts last weekend and which were blamed on ETA. They caused no injuries and little damage.
Beaches at an eastern Spanish resort were evacuated briefly on Wednesday after what appeared to be a false bomb alert.
The rash of bomb alerts - days after the government warned ETA bombers may be aiming to strike at the tourism industry - has fuelled uneasiness in Spain.
ETA regularly stages summer bombing campaigns in an attempt to undermine Spain's tourism industry which accounts for more than a tenth of its economy.
The group, branded a terrorist organisation by the European Union and the United States, has not carried out a fatal attack for more than a year.