During the Second World War, resistance movements that bore any resemblance to irregular warfare were frequently dealt with by the German occupying forces under the auspices of anti-partisan warfare. In many cases, the Nazis euphemistically used the term "anti-partisan operations" to obfuscate ethnic cleansing and ideological warfare operations against perceived enemies; this included Jews, Communist officials (so-called Jewish Bolsheviks), Red Army stragglers, and others. This was especially the case on the Eastern Front, where anti-partisan operations often resulted in the massacres of innocent civilians. While the worst atrocities in terms of scale occurred in the Eastern theater of the war, the Nazis employed "anti-partisan" tactics in Western Europe as well.

Historian Alex J. Kay estimates that around one million civilians may have died as a result of German anti-partisan warfare—excluding actual partisans—among the 13 to 14 million people murdered by the Nazis during World War II.

A. Dirk Moses notes that the German security warfare was an extreme version of strategies and tactics pursued by other colonial powers against anti-colonial resistance. "All resistance was regarded as illegitimate, and civilians were targeted preemptively and often collectively to forestall future resistance", while the laws of war were suspended on the basis that the enemy was barbarian.

The forms of resistance varied depending on place and time, and so did the Germans' countermeasures. Both the scale of resistance and the severity of German reprisals were much more limited in the West than in the East. While Germans were much more likely to treat the entire local populace as enemies in the East, they were much less ideologically driven in the West, where, for example, women and children were only rarely killed by SS troops, but a much more common target in the East. Some scholars have noted that in the East, the anti-partisan operations gave Germans a pretext for ideologically motivated ethnic cleansing.

In the context of the German campaign against so-called "partisans" in the occupied territories, SS Chief Heinrich Himmler framed security operations as a struggle for the survival of the Reich. He cast local resistance not as legitimate military opposition but as a form of criminality threatening the German people, thereby justifying draconian measure. As he explained in December 1941:

The task entrusted to us is to guarantee security, law and order... This task demands of us that we eliminate ruthlessly every center of resistance and impose in the most drastic way the just death penalty upon the enemies of the German people.

The Germans concentrated on short-term victories against the partisans and were able, in some cases, to defeat the partisans militarily, but overall their atrocities against civilians in the East resulted in a continuous flow of volunteers joining the partisan ranks. The first resistance movements were created as early as late 1939 in occupied Poland (see the Separated Unit of the Polish Army). As the war progressed and the number of Nazi-occupied territories grew, so did the number and strength of resistance movements.

Throughout the war, regular formations of German army, auxiliary police formations (Ordnungspolizei) and their helpers (Schutzmannschaft or Hilfspolizei) participated in anti-partisan operations. The struggle of Germans versus the partisans can be described as a stalemate, eventually ended by the German military defeat in the regular war. After the war, brutal German tactics used against the partisans were one of the charges presented at the Nuremberg Trials (see legality of the Commando Order and Hostages Trial).