diff --git a/src/libslic3r/Layer.cpp b/src/libslic3r/Layer.cpp
index 2fa0c5c3c..35b4a331a 100644
--- a/src/libslic3r/Layer.cpp
+++ b/src/libslic3r/Layer.cpp
@@ -317,13 +317,16 @@ void Layer::build_up_down_graph(Layer& below, Layer& above)
             coord_t* end = srcs + 4;
             std::sort(begin, end);
             end = std::unique(begin, end);
-            assert(begin + 2 == end);
-            if (begin + 1 == end)
+            if (begin + 1 == end) {
+                // Self intersection may happen on source contour. Just copy the Z value.
                 pt.z() = *begin;
-            else if (begin + 2 <= end) {
-                // store a -1 based negative index into the "intersections" vector here.
-                m_intersections.emplace_back(srcs[0], srcs[1]);
-                pt.z() = -coord_t(m_intersections.size());
+            } else {
+                assert(begin + 2 == end);
+                if (begin + 2 <= end) {
+                    // store a -1 based negative index into the "intersections" vector here.
+                    m_intersections.emplace_back(srcs[0], srcs[1]);
+                    pt.z() = -coord_t(m_intersections.size());
+                }
             }
         }
         const std::vector<std::pair<coord_t, coord_t>>& intersections() const { return m_intersections; }
diff --git a/src/libslic3r/PerimeterGenerator.cpp b/src/libslic3r/PerimeterGenerator.cpp
index 490fd54bf..875870fa8 100644
--- a/src/libslic3r/PerimeterGenerator.cpp
+++ b/src/libslic3r/PerimeterGenerator.cpp
@@ -397,22 +397,37 @@ static ClipperLib_Z::Paths clip_extrusion(const ClipperLib_Z::Path &subject, con
     ClipperLib_Z::Clipper clipper;
     clipper.ZFillFunction([](const ClipperLib_Z::IntPoint &e1bot, const ClipperLib_Z::IntPoint &e1top, const ClipperLib_Z::IntPoint &e2bot,
                              const ClipperLib_Z::IntPoint &e2top, ClipperLib_Z::IntPoint &pt) {
+        // The clipping contour may be simplified by clipping it with a bounding box of "subject" path.
+        // The clipping function used may produce self intersections outside of the "subject" bounding box. Such self intersections are 
+        // harmless to the result of the clipping operation,
+        // Both ends of each edge belong to the same source: Either they are from subject or from clipping path.
+        assert(e1bot.z() >= 0 && e1top.z() >= 0);
+        assert(e2bot.z() >= 0 && e2top.z() >= 0);
+        assert((e1bot.z() == 0) == (e1top.z() == 0));
+        assert((e2bot.z() == 0) == (e2top.z() == 0));
+
+        // Start & end points of the clipped polyline (extrusion path with a non-zero width).
         ClipperLib_Z::IntPoint start = e1bot;
         ClipperLib_Z::IntPoint end   = e1top;
-
         if (start.z() <= 0 && end.z() <= 0) {
             start = e2bot;
             end   = e2top;
         }
 
-        assert(start.z() > 0 && end.z() > 0);
+        if (start.z() <= 0 && end.z() <= 0) {
+            // Self intersection on the source contour.
+            assert(start.z() == 0 && end.z() == 0);
+            pt.z() = 0;
+        } else {
+            // Interpolate extrusion line width.
+            assert(start.z() > 0 && end.z() > 0);
 
-        // Interpolate extrusion line width.
-        double length_sqr = (end - start).cast<double>().squaredNorm();
-        double dist_sqr   = (pt - start).cast<double>().squaredNorm();
-        double t          = std::sqrt(dist_sqr / length_sqr);
+            double length_sqr = (end - start).cast<double>().squaredNorm();
+            double dist_sqr   = (pt - start).cast<double>().squaredNorm();
+            double t          = std::sqrt(dist_sqr / length_sqr);
 
-        pt.z() = start.z() + coord_t((end.z() - start.z()) * t);
+            pt.z() = start.z() + coord_t((end.z() - start.z()) * t);
+        }
     });
 
     clipper.AddPath(subject, ClipperLib_Z::ptSubject, false);