In December of 1942 the Germans appointed Rabbi Zvi Koretz as head of the Jewish Community. In February 1943, Dieter Wisliceny, Eichmann's deputy, arrived in Salonica to set the machinery for deportation. Jews were ordered to wear Star of David badges and to move into ghettos and were subjected to a wide variety of other restrictions.

Deportations began in March 1943 from Macedonia and Thrace while at the same time Bulgarians were assisting the Germans in deporting the Greek Jews from the territory they had annexed. "The German Reich is ready to accept these Jews in its eastern regions," said the agreement signed by Bulgaria on February 22. A month after this agreement was signed, "these Jews" were dead.

Ten thousand Jews had been deported by the end of March 1943, a further 25,000 in April and another 25,000 in May. They had no idea of their destination having been told that it was a "resettlement" area in Poland.

A notable exception to the deportation of the Macedonian Jews was the town of Katerini. The local director of police gave Jews three hours to flee after he received the deportation orders. Thirty-three Jews fled and were hidden by Greek villagers. Three who were unable to leave, were shot by the Germans when they discovered that almost all the community had escaped.

Each deportee was allowed to take a food parcel for the journey and up to 15 kilos of clothing for the "resettlement" area. It was in fact Treblinka or Birkenau. The Germans allocated 20 special trains for these deportations starting from six collection points. At the railway stations of Demi-Hisar and Simitli, where there was a change of trains, the Germans gave priority to "invalids on strectchers" and women who were "ready for childbirth." Conditions inside the trains were horrific: no room to sit or lie down, virtually no food and no water.

Each morning on their journey north the trains would stop in the open countryside and the bodies of those who died in the night were thrown out. There was no form of burial allowed. Several hundred sick and old people died during the six day journey.

Shortly after the deportations, all Jewish property and belongings in Thrace and Macedonia were confiscated and sold. The money raised was first to go towards the cost of the rail fare to the death camps. The rest was then deposited in bank accounts and to give those still in Greece a sense of normalcy, the deposit statements were sent to their Jewish owners. These statements reached their owners long after they were dead in Treblinka and Auschwitz.

On April 5, 1943, the last train bringing Jews from Macedonia for "resettlement" reached Treblinka. All were gassed.

In September 1943, when all of Greece came under German control, general anti-Jewish regulations were issued, defining who is a Jew and ordering Jews to register. Jews who did not report to the Germans within five days would be shot, and any Greek providing shelter to Jews would be shot as well. Within six months the deportations of Jews from Athens began and the Germans began to round up Jews on the islands.