Iran had tried to put off the mission earlier this month after the IAEA condemned it for continuing to hide sensitive nuclear activities.
But Tehran yielded and allowed the visit, delayed by two weeks, after an international outcry against Iran for failing to cooperate with the atomic agency.
The inspectors will be "leaving on Saturday for Iran for an inspection mission to the Natanz and Isfahan facilities," IAEA spokeswoman Melissa Fleming said.
The Natanz uranium enrichment plant is one of two sites where IAEA inspectors have discovered traces of highly enriched uranium, a substance which can be used both in civilian reactors to generate electricity and also as the raw material for a nuclear bomb.
Isfahan is a nuclear technology center, with a uranium conversion facility where the IAEA has safeguards.
A diplomat close to the IAEA said this inspection visit was "routine, nothing spectacular."
He said the IAEA would not be verifying on this trip Iran's suspension of uranium enrichment.
Iran promised in February to halt not just enriching uranium but all related activities, such as building centrifuges, in a move IAEA chief Mohamed ElBaradei said was crucial to Iran's building confidence in its full cooperation.
The diplomat said another inspection team slated to go into Iran in perhaps two weeks would be looking more aggressively for new findings.
The diplomat said the IAEA was still operating under two different agreements, one for safeguard inspections under the nuclear Non-Proliferation Treaty (NPT) and the other under an additional protocol to the NPT which allows for snap, short-notice inspections which Iranian authorities are obliged to accept.
The IAEA has since February 2003 been verifying whether Iran's nuclear programme is peaceful, or devoted to secretly developing atomic weapons, as the United States claims.
The European Union called on Iran Monday to come completely clean on its nuclear programme.
The EU, which favours "constructive engagement" with Iran, has been more cautious in its appraisal of Tehran's nuclear drive.
ElBaradei had said in Washington March 17 that he still could not rule out finding that Iran has been hiding a nuclear weapons program.
He told a US congressional subcommittee that Iran was developing a nuclear fuel cycle as it has been under international sanctions against its nuclear program.
"Have they taken the step from that into weaponisation? We have not seen that but I am not yet excluding that possibility," ElBaradei told the subcommittee on Middle East and Central Asian affairs.
"The jury is still out," on whether Iran possesses such a program, he said.
He said the IAEA's discovery in January of designs for sophisticated P2 centrifuges in Iran for making highly enriched uranium was "a setback, a great setback" since Iran claimed in October it had fully disclosed its nuclear activities.
This led to the tough resolution against Iran at an IAEA board of governors meeting in Vienna last week for hiding sensitive nuclear activities.