UPDATE: Good news finally: Greece's Aegean Airlines (http://www.aegeanair.com), a member of the Star Alliance, will launch a direct Athens-Istanbul (Ataturk) daily service, with effect from 09 September 2009. For those who want to visit both Istanbul and the Cyclade Islands within a few days, there is now the option of flying from Istanbul to Mykonos, Santorini, Naxos etc. via Athens.
If you are in Thessaloniki or anywhere in Northern Greece (the province of Macedonia, Thessaly, Thrace) and you want to go to Edirne, Istanbul or anywhere along the Black Sea coast of Turkey, then it is easier to go by bus.
UPDATE: As of January 2011, all train services between Istanbul and Thessaloniki have been suspended.
A) BY BUS: Turkish bus companies Varan and Ulusoy operate long distance inter-city bus that departs Athens, Larissa, Thessaloniki, Alexandroupolis in Greece and drops off passenger at Edirne or Kesan en route to Istanbul.

Check up time-table and schedule at:
http://www.varan.com.tr
http://www.ulusoy.com.tr

Apparently Kamil Koc also operates long distance bus between Greece and Istanbul, but their website does not offer any international time-table. It is advisable to ask details about price and availability at one of their offices in Turkey.
http://www.kamilkoc.com.tr

UPDATE: As of January 2011, all train services between Istanbul and Thessaloniki have been suspended.
B) BY TRAIN: Turkish national train operator TCDD and Greek national train company OSE operate two trains per day between Thessaloniki and Istanbul Sirkeci Station, one in the morning and one in the evening, stopping en route at Pithion (Greek border town), Alexandroupolis, Komotini, Drama, Serres, Thessaloniki. Passengers travelling onwards to Athens and Larissa should disembark at Thessaloniki and change to Greek InterCity trains. There are no direct Istanbul - Athens trains as of now.
The train is, however, much slower than inter-city buses and are prone to long delays, especially at the border crossings between Greece and Turkey.
The morning train that departs Istanbul Sirkeci Station has coaches with normal seats. The train only runs as far as the Greek border station of Pithion. Only one passenger coach will cross the border to Pithion, the rest of the train will be uncoupled at Uzunköprü (Turkish border station). Make sure you are on the coach that goes through to Pithion.
Passport checks: First you need to disembark at
Uzunköprü to get a Turkish exit stamp. Then get on the train again and disembark again once the train arrives at Pithion station to pass through Greek passport control and customs.
After passing through Greek border formalities, there will be a Greek intercity train waiting for Thessaloniki-bound passengers on the platform. The original Turkish train + coach will return across the border to Uzunköprü and Istanbul.
NOTE: AS OF JUNE 2008, THE MORNING TRAIN SERVICE BETWEEN PITHION AND THESSALONIKI IS SUSPENDED DUE TO ENGINEERING WORKS AT ALEXANDROUPOLIS STATION. PART OF THE JOURNEY PITHION - THESSALONIKI WILL BE REPLACED BY BUS INSTEAD. PLEASE CHECK WITH OSE FOR FURTHER DETAILS.
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Night Train from Istanbul - Thessaloniki (FILIA /DOSTLUK EXPRESS = Friendship Express )
This train consists only of sleeping compartments and berths. No coaches with ordinary passenger seats. The train departs Istanbul Sirkeci Station shortly after 2000 and the whole train will cross the Greco-Turkish border shortly after midnight and continue westwards till Thessaloniki, arriving at around 0700 in the morning. Passengers still need to disembark at Uzunköprü and Pithion respectively to complete passport and customs formalities, but there is no need to change to another Greek train at Pithion.

Check up time-tables at:
TCDD (Turkish National Railways)     http://www.tcdd.gov.tr
OSE (Greek National Railways)         http://www.ose.gr

C) BY AIR: well, finally there are some shake-ups on the lucrative Athens-Istanbul flight route. With effect from 09 September 2009, Aegean Airlines, a member of the Star Alliance, will launch a daily service between Istanbul and Athens. This means the duopoly previously held by the usual suspects - Turkish Airlines and Olympic Airways - will cease to exist. Good news for those who have little time on time yet want to spend a few days on one of the Greek islands. If you book early enough, you can fly to places such as Santorini or Mykonos via Athens from Istanbul for much less than what you would have to pay on other airlines.
UPDATE (Aug 2009): Another piece of good news for those who want to fly non-stop from Athens to Izmir. Turkish Airlines will launch a non-stop direct flight Izmir - Athens - Izmir, without the need for a stop-over in Istanbul. The flight takes about 1 hour. However, it departs Izmir early in the morning at 06:00, arriving back in Izmir at 00:20 shortly after midnight. For those who don't mind getting up early and want to be in Athens really early in the morning, this is a viable alternative to the Izmir - Cesme - Chios (Ferry) - Piraeus (Ferry) connection.
See my post  http://hert1302.pixnet.net/blog/post/25692535 for detail flight times etc.
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Sometimes (i.e. depending on the circumstances), between mid-June and mid-September, Atlasjet, a private airlines from Turkey, operates 2-3 charter flights a week between Istanbul and Mykonos/Santorini. However, you can't book Istanbul - Mykonos or Istanbul - Santorini tickets online on Atlasjet's website. These tickets can only be bought by calling Atlasjet's service centre in Turkey, or via a travel agent in Turkey.
Normally these charter flights are for package tour groups, but they will also accept individual passenger bookings if there are sufficient seats available.
As of May 2009, it is not yet clear if the time-table and price for Istanbul-Mykonos and Istanbul - Santorini flights are already available, or indeed if Atlasjet will operate these routes this year. I would say Aegean Airlines are a safer bet. Good luck!!

For those who are on one of the Greek Cyclade islands (e.g. Mykonos, Santorini, Naxos, Paros, ...etc.) or Crete, and want to go to northern Turkey, it might be useful to fly to Alexandroupolis, a Greek city about 50-70km from the Greco-Turkish border., via Athens.
From Alexandroupolis you can:
A) take inter-city buses that will take you direct to Istanbul, Edirne or Kesan in Turkey, from where there are frequent bus links to cities and towns all over Turkey, including Ankara, Canakkale and Izmir.
B) take the train (or replacement bus service) from Alexandroupolis to Pithion, then change to the Turkish train bound for Istanbul.

Copyright 2008. All text by YC Cheng. All information compiled by YC Cheng. All Rights Reserved.

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