The American military says it struck 170 targets across the two waves of attacks.
On Tuesday, Iran's military said eight of its soldiers were killed in Tuesday's strikes, with targets clustered around the coastline of the Strait of Hormuz.
Kuwait and Bahrain said their air defenses were responding “hostile missile and drone attacks” early Thursday, hours after the Iranian military vowed to hit back in response to another round of US airstrikes against Iran.
“The General Staff of the Army notes that any explosions heard are a result of air defense systems intercepting hostile attacks,” the Kuwait military said in a post on X, without specifying their origin.
Explosions were heard in Bahrain’s capital on Thursday, an AFP correspondent in Manama said, moments after authorities sounded air raid sirens to warn of an attack.
Qatar also issued an alert but the Ministry of Interior, in a statement carried by the Qatar News Agency, later announced “the end of the security threat.”
The attacks came after Iran’s Revolutionary Guards vowed to retaliate following another round of US strikes on Iranian territory.
Iranian state media later reported that the Guards had launched missiles and drones targeting two US military bases in Kuwait and two in Bahrain.
A day earlier, Kuwait’s military said it had intercepted two missiles and 13 drones launched from Iran, underscoring the growing frequency of cross-border attacks as the confrontation between Tehran and Washington intensifies.
The latest strikes follow Iranian attacks earlier this week on US military facilities in Kuwait and Bahrain, which drew widespread international condemnation and heightened concerns that the conflict could spread across the Gulf.
Saudi Arabia strongly condemned the attacks, describing them as violations of the sovereignty of Kuwait and Bahrain and breaches of international law. The Kingdom called on Iran to immediately halt what it described as repeated acts of aggression and warned that continued escalation threatened regional security and stability.
The United Arab Emirates, Qatar, Jordan, Egypt and Oman also condemned the earlier attacks, urging restraint and renewed diplomatic efforts to prevent a wider regional conflict. China likewise called on both Washington and Tehran to avoid reigniting war and to return to dialogue.
The latest exchange comes as regional mediation efforts face mounting pressure after recent US-Iran understandings appeared to unravel following renewed military action. The conflict has also disrupted shipping through the Strait of Hormuz, where Iranian attacks on commercial vessels in recent days have further raised concerns over the security of one of the world’s busiest energy corridors.
Three people have been killed in US strikes in western Iran earlier this morning, according to the Fars state news agency.
The damage in the city of Ahvaz, in Khuzestan province, was still under investigation, the region's deputy governor said.
Elsewhere, passenger trains were stopped on a major route between the cities of Tehran, the capital, and Mashhad after a railway line was struck in a separate attack, the news agency reported.
Reconstruction operations are under way at the damaged site, with efforts being made to repair the route "in the shortest possible time."
Earlier, US Central Command said "air defence systems, coastal surveillance assets, missile and drone storage sites, naval capabilities, and military logistics infrastructure along Iran's coastline" had all been targeted in its strikes last night.Trump: Iran 'called a little while ago' and want to make a deal
Donald Trump has been travelling back to the US from the NATO summit in Ankara.
Speaking to reporters aboard Air Force One, the US president said the Iranian leadership had called him and indicated they wanted to make a deal.
"They called a little while ago. They want to make a deal so badly," he said.
Trump's comments come after the US military struck more than 90 targets in Iran last night.
Asked about the strikes, he said "it was really retribution."
Trump made a brief stop in the UK on the way home from the NATO summit last night, but denied security fears were behind the decision.
The president changed planes at RAF Mildenhall in Suffolk, continuing his journey home from Ankara on the new Air Force One that was given to him by Qatar.
Asked by reporters after resuming the journey if he was aware of credible threats to the plane, Trump said: "I have a threat all the time. I’m number one of their list."
The second consecutive night of US strikes on Iran lasted a pretty significant period of time and looked "more wide ranging", our Middle East correspondent Adam Parsons says.
"[But] what is notable, I think, at the moment is that so far, there's no evidence of missiles being fired towards Israel or Israel's military taking any part in this at all," he reports from Jerusalem.
"It seems at the moment to be solely between the United States and Iran."
The number of missiles Iran is firing in response - around 90 last night - undermines Donald Trump's suggestion that its military had been almost completely destroyed, Parsons says.