I want to intersect two layers (shapefiles) with QGIS 2.18. For both layers, I tested validity with

  • QGIS Vector / Vector Tools / Check validity and
  • GRASS v.build.check (with default parameters)

both tests report no errors for both layers, but QGIS Intersection reports invalid geometry for one or more input features.

The two layers may have some boundaries, that should be equal, but may actually have slight differences (unprecise manual digitalisation of one layer) possibly resulting in several very small slices.

What do you recommend me to try?

  • 1
    QGIS builds the difference between the two layers without error message and gives more than 100 areas smaller than 0.5 m2.
    – Bartli
    Commented Dec 28, 2017 at 12:06
  • 1
    What's the type of the geometries? Polygons? Both have the same coordinate reference system?
    – pnz1337
    Commented Dec 28, 2017 at 14:02
  • @pnz Yes, polygons. Both have the same coordinate system.
    – Bartli
    Commented Dec 28, 2017 at 17:31

4 Answers 4


SAGA - vector polygon tools - intersection is my friend. It creates a new Layer without stopping because of errors. Now, I have to delete features with small areas from the new layer.


Maybe this works (Fixing invalid polygon ..):



Or another problem could be that, you have multipolygons, therefore you have to explode them before intersecting:

Vector / Geometry Tools / Multipart to Singleparts

  • This felt like a good starting point to me, but it did not solve the problem. An explanation as to why this might be the cause could be helpful.
    – gktscrk
    Commented Oct 27, 2019 at 11:11

Saga gis intersect works, from my experience, as long as intersect does not include any of the faulty polygons. For me worked Fix geometry tool in QGIS3. I suspect in my case the problem was self intersecting poygons. Similar issue: Intersection error QGis - invalid geometries that are actually valid.

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