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I have two shapefiles containing each one set of points, set A and set B. One set is my random selection (set A), the other is a list of communities (set B).

For each point of the random selection (set A) I want to find the nearest point pertaining to

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is your set B a list of centroids? –  Kurt Sep 16 '12 at 9:02
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You could use GRASS' v.distance via the Sextante plugin. It calculates all these distances.

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