The former KGB official called the Vatican stop "a very significant visit" that he had insisted on making at the onset of his presidency.
While there was no report of progress on a long-sought papal trip to Russia--and no new invitation from Putin for a visit--the pope's spokesman said the invitation first issued by Soviet President Mikhail Gorbachev in 1989 still stands.
Although Putin showed up 20 minutes late, the breach of protocol didn't seem to upset the businesslike atmosphere.
The Russian official's meeting with the pontiff came on the first day of a two-day Italian trip, designed to allow Putin to reach out to Western European leaders on such issues as a possible joint anti-missile defense that would not breach the 1972 Anti-Ballistic Missile Treaty.
In his meeting with John Paul, Putin was hoping to escape Vatican admonitions about Russia's war in Chechnya. Putin apparently succeeded in that.
There was no mention of Putin's uncompromising stand on Chechnya in the bland Vatican communique on the 50 minutes of talks that included a half-hour one-on-one with John Paul with only interpreters present.
The pope's spokesman, Joaquin Navarro-Valls, said John Paul mainly listened as Putin described his mission of enlisting Vatican help in "the process of integration between east and west."
Security was tight around the Vatican, with police stationed at major streets near St. Peter's Square. A police helicopter flew overhead as Putin's motorcade entered the Vatican.
In greeting Putin, John Paul said, "I am very happy to receive you at the Vatican at the beginning of your mandate."
Navarro-Valls was cautious about the prospects of a trip to Russia, long dreamed of by John Paul in his bid for reconciliation between Roman Catholics and Orthodox Christians.
The spokesman did note the more positive tone from the Moscow patriarch, Alexey II, over the weekend, which contrasted with recent and often repeated harsh accusations that the Vatican is seeking to win converts in traditional Orthodox territory.
Putin gave the pope a book on the restoration of the Kremlin; John Paul in turn presented the president with a bas-relief of Saints Peter and Paul.
Putin paid his first Western visit in April, to Britain, while still acting president after Boris Yeltsin's resignation. The inauguration for Putin's own elected term came in May.