The 83-year-old pontiff's plane landed at an Adriatic island airport, where the ex-Yugoslav republic's president and top church leaders welcomed him.
"I thank Almighty God for having allowed me to come back among you on this, my hundredth pastoral visit," John Paul said to applause.
His theme is going to be family, reports CBS News Correspondent Allen Pizzey, but he'll also talk about reconciliation and forgiveness of the past. Croatian suffered a pretty horrific war in the early 1990s.
Although his left arm shook and he gulped deep breaths, the pope delivered his arrival speech in Croatian with a strong and clear voice before being spirited by high-speed catamaran across a bay to Rijeka's harbor, where thousands of cheering pilgrims gathered near the docks to greet him.
Earlier, as he boarded the Alitalia flight in Rome, John Paul had difficulty walking and had to be helped by aides onto the special lift he uses to get on and off aircraft. The Italian airline presented the pope with a special cake in honor of his 100th trip.
John Paul's visit, which gets into full swing Friday with a visit to the war-battered southern coastal resort of Dubrovnik, will test anew his ability to overcome his advanced age, Parkinson's disease, hip and knee troubles and balmy summer weather.
He is the most traveled pope in the history of the Catholic Church, reports Pizzey. He's been now the equivalent of to the moon and back and back to the moon again — about 30 times around the world, in fact.
It's his third trip to Croatia.
The pope expressed his affection for this overwhelmingly Catholic country, praising "the ancient Christian roots of this land steeped in the blood of countless martyrs."
About 80 percent of Croatia's 4.5 million people are Roman Catholics, and the Vatican was among the first to recognize the country's statehood in January 1992, six months after it declared independence from Yugoslavia.
For most Croats, the pope is the highest moral authority. Half a million faithful are expected to attend papal Masses in Rijeka, Dubrovnik, the southern coastal city of Zadar and the eastern cities of Osijek and Djakovo.
Croats "greet you with smiles, joyful hearts and open arms," President Stipe Mesic told the pontiff. "Aware of problems that are the legacy of history, war and our own limitations, we today want to pursue democracy, to build a just society."
The pope's return visit "shows how much the Holy Father cherishes Croatia, its church and its people," said Ivan Devcic, bishop of the port city of Rijeka, which will serve as a base for the pope and his entourage.
Photographs of John Paul are in shop windows and on billboards all over Croatia. Schools were closed in honor of his visit, and many Croats intended to skip work to see him. Security was tight for the pope's arrival, with automobile traffic restricted in the cities awaiting him, but trains were available free of charge to pilgrims.
"The pope will bring us spiritual peace, and we need it," said Ana Brnabic, a 52-year-old worker.
John Paul first came here in 1994, just three years after a devastating war with the local Serbs who rebelled against Croatia's declaration of independence. He returned in 1998 to preach postwar reconciliation and tolerance.
This time, the pope will find a country caught between its desire to finally join the West and the lingering nationalism that threatens to keep it isolated.
War veterans and many ordinary Croats oppose the U.N. war crimes tribunal's prosecutions of Croat fighters whom they hail as war heroes. Minority Serbs, who fled the country in 1995 when it retook areas the rebels seized in 1991, are generally not welcome back.
Some youngsters carry memorabilia of Croatia's World War II Nazi puppet state. The nationalist party founded by the late President Franjo Tudjman enjoys 25 percent support and could even win elections this fall.
Wading gingerly into the fray, John Paul is expected to call anew on Croats to pursue tolerance, reconciliation and coexistence.
But his visit is mainly intended to show support for Croats' persistent faith and the nation's efforts to become a part of the European mainstream. The pope often has encouraged Croatia's efforts to join the European Union, a prize some leaders hope to win as early as 2007, and he did so again Thursday.
"Croatia has recently asked to become an integral part ... of the great family of the European peoples," John Paul said. "I can only express my hope that that this aspiration will be happily realized."