At that point, passengers are given a sticker with a number on it ranging from one through six; the higher the number, the higher the risk factor.
All luggage then goes through an X-ray machine while passengers pass through metal detectors. Afterwards, passengers can either proceed to their gates or they are sent to a room where officials hand-check everything in their suitcases.
Passengers that were earlier flagged as a five or six have their suitcases taken apart and swabbed, a process that could take 45 minutes.
High-risk passengers also may be led to a room for a full-body pat-down, which involves disrobing to their underwear.
Then it is off to immigration, where there is another check of hand luggage and one more pass through a metal detector.
For low-risk passengers, the security procedure is not much of a hassle. Josh Tapper, 23, recently travelled from New York to Israel. He said security measures in Israel are comparable with what he has experienced in the U.S.
"They're both a hassle, but one no more than the other," he said.
However, Tapper added that passengers who are not obviously Jewish or look Arab face much tougher security.
That type of passenger might include Daoud Kuttab, 55, who travels frequently between Europe, the U.S. and Amman, Jordan. The director of a media non-governmental organization avoids Tel Aviv's airport whenever possible.
Kuttab said there is no comparison between security in Israel and that in the U.S.
"I think the American system is much more scientific, much more logical," said Kuttab. "It's not even an argument for me. The U.S. system, while with its problems, is much more humane and logical and non-intrusive."
According to Ron, the security consultant and former Tel Aviv security chief, Israel is thinking of adding a more scientific approach to its security methods. He said Ben Gurion Airport has started using body scanners, but has not yet included them in standard procedure.
Back in the U.S., the TSA may want to go G-rated with its full-body scans, but the technology isn't there yet.
In a Senate hearing Wednesday, TSA administrator John Pistole said the new scanners are generating too many false positives. Therefore, the TSA is hesitant to confirm a rollout date, though Boston's TSA security director, George Naccara, told a local paper that Logan International Airport is set to be the first to get the new "stick figure" scanners by late winter.
ABC News' Matt Hosford in Washington and Simon McGregor-Wood in Jerusalem, and the Associated Press contributed to this report.