Israel's main entry point for the international traveller, the newly built Terminal 3 at Ben Gurion International Airport, named after Israel's first Prime Minister, is situated near Lod and next to the highway linking Tel Aviv and Jerusalem. The airport, referred to by locals as Natbag  its initials in Hebrew  comprises all the usual amenities expected from a first class airport and contains one of the world's largest duty free shopping malls for an airport of its size. Ben Gurion Airport acts as the base for El Al, Israel's national airline, and is also served by over 50 international air carriers. Travel from the airport to the centre of Jerusalem takes 40;50 minutes and depending on traffic conditions often more. It is advisable to budget at least an additional 2 hours on top of your pre flight check in time to ensure timely arrival and completion of security procedures.
Security is extremely stringent at Ben Gurion Airport, and is especially suspicious of travelers with Muslim names or visas from Islamic countries in their passports. Expect to be stopped and questioned for several hours if this is the case, both on the way in and on the way out. It would be wise to have some phone numbers of local contacts for security officials to call to verify your reasons for visiting. The airport prides itself in being one of the most secure in the world. It achieves this through a number of means. The most evident for travellors will be the pre checking security check. On joining the queue for this security check, a security official will ask you several questions. Based on these and a brief inspection of your passport, you will be asigned a number from 1 to 6. 1 signifies the lowest security concern and 6 the highest. Foreigners will typically get between a 3 and a 6. Age, appearance, stamps from Arab countries, evidence of visits to the Palestinian territory and other vague factors will be taken into account. Depending on the number you get, the security check is more or less thorough. Travelers who have visited the Palestinian territory and state as much will almost certainly receive a 5 or 6. With a 5 or a 6, you can expect every single item of luggage to be taken from you bag and inspected in detail. Security officials have been known to check individual bank-notes. With a 6, you can also expect to be taken to a cubicle and asked to remove your belt, shoes and have a personal inspection. If your clothes contain any metal that would set off a detector even if plainly visible on the outside, you will be asked to remove the item of clothing. Travelers are regularly prevented from taking mobile phones, laptops and even shoes in their hand-luggage, although there is no consistency with reports of one policy one week and another the next week. Arguing about such invasive checks is almost always fruitless and security reasons are the only ones that are ever cited. This summary is based on personal experiences.
Getting to and from Jerusalem. The 'Nesher' shared taxi service  is a 14 seater minibus that runs approximately hourly services to the airport  55 NIS one way per person. You must reserve your seat in advance by phone and you will be picked up from your hotel or a chosen location. Be on time they don't wait. You will be dropped at Terminal 3 in the airport. For the journey to Jerusalem, you will find them waiting outside the arrivals hall. Tell the driver where you want to be dropped. Again they should drop you at your hotel, but have been known to avoid parts of East Jerusalem. The rate is fixed, but it is worth double checking as it has recently increased.
A private taxi to/from Jerusalem will cost around 150;200 NIS.