The German and Slovak government agreed in early 1942 that Germany would take all of Slovakia’s Jews in return for a certain payment. During the first phase in March and April, only Jews fit for labor were deported to the labor camps of Majdanek and Auschwitz. Starting in late April 1942, everyone was deported, including entire families. Those fit for work were admitted into the Majdanek or Auschwitz camps, whereas the rest was sent on to various camps and ghettos, and since late May 1942 also directly to Sobibór for moving them further east.
When in July 1942 military necessities did not allow sending deportation trains with civilians east, everyone was sent to Auschwitz, with some deportees not getting registered in the camp, either because they had been taken off elsewhere or were continuing their journey. The orthodoxy insists that they were gassed on arrival, though. During these 1942 deportations, altogether not quite 48,000 Jews were deported from Slovakia.
A second wave of deportations occurred in September 1944, after the brief German occupation of Slovakia. Some 13,000 to 14,000 are said to have been deported within a few months. Some 7,000 to 8,000 of them presumably ended up at Auschwitz, while the rest was deported to German labor camps, such as Ravensbrück and Sachsenhausen.
In total, some 61,000 – 62,000 Jews were deported from Slovakia during the war. (See the entry on Jewish demography for a broader perspective.)