diff --git a/document.h b/document.h
index d4d8ce8..1c28586 100644
--- a/document.h
+++ b/document.h
@@ -77,7 +77,9 @@ zathura_image_buffer_t* zathura_image_buffer_create(unsigned int width, unsigned
 void zathura_image_buffer_free(zathura_image_buffer_t*);
 
 /**
- * Rectangle structure
+ * Rectangle structure.
+ * The coordinate system has its origin in the left upper corner. The x axes
+ * goes to the right, the y access goes down.
  */
 typedef struct zathura_rectangle_s
 {
diff --git a/page_widget.c b/page_widget.c
index cf0335c..1b110be 100644
--- a/page_widget.c
+++ b/page_widget.c
@@ -292,7 +292,7 @@ zathura_page_widget_expose(GtkWidget* widget, GdkEventExpose* event)
         /* draw text */
         cairo_set_source_rgba(cairo, 0, 0, 0, 1);
         cairo_set_font_size(cairo, 10);
-        cairo_move_to(cairo, rectangle.x1 + 1, rectangle.y1 - 1);
+        cairo_move_to(cairo, rectangle.x1 + 1, rectangle.y2 - 1);
         char* link_number = g_strdup_printf("%i", priv->link_offset + ++link_counter);
         cairo_show_text(cairo, link_number);
         g_free(link_number);
@@ -384,9 +384,9 @@ redraw_rect(ZathuraPage* widget, zathura_rectangle_t* rectangle)
    /* cause the rect to be drawn */
   GdkRectangle grect;
   grect.x = rectangle->x1;
-  grect.y = rectangle->y2;
+  grect.y = rectangle->y1;
   grect.width = rectangle->x2 - rectangle->x1;
-  grect.height = rectangle->y1 - rectangle->y2;
+  grect.height = rectangle->y2 - rectangle->y1;
   gdk_window_invalidate_rect(GTK_WIDGET(widget)->window, &grect, TRUE);
 }
 
diff --git a/utils.c b/utils.c
index 27926b8..a89d852 100644
--- a/utils.c
+++ b/utils.c
@@ -200,28 +200,28 @@ recalc_rectangle(zathura_page_t* page, zathura_rectangle_t rectangle)
 
   switch (page->document->rotate) {
     case 90:
-      tmp.x1 = rectangle.y2 * page->document->scale;
-      tmp.x2 = rectangle.y1 * page->document->scale;
+      tmp.x1 = (page->height - rectangle.y2) * page->document->scale;
+      tmp.x2 = (page->height - rectangle.y1) * page->document->scale;
       tmp.y1 = rectangle.x1 * page->document->scale;
       tmp.y2 = rectangle.x2 * page->document->scale;
       break;
     case 180:
       tmp.x1 = (page->width - rectangle.x2) * page->document->scale;
       tmp.x2 = (page->width - rectangle.x1) * page->document->scale;
-      tmp.y1 = rectangle.y2 * page->document->scale;
-      tmp.y2 = rectangle.y1 * page->document->scale;
+      tmp.y1 = (page->height - rectangle.y2) * page->document->scale;
+      tmp.y2 = (page->height - rectangle.y1) * page->document->scale;
       break;
     case 270:
-      tmp.x1 = (page->height - rectangle.y1) * page->document->scale;
-      tmp.x2 = (page->height - rectangle.y2) * page->document->scale;
-      tmp.y1 = (page->width  - rectangle.x2) * page->document->scale;
-      tmp.y2 = (page->width  - rectangle.x1) * page->document->scale;
+      tmp.x1 = rectangle.y1 * page->document->scale;
+      tmp.x2 = rectangle.y2 * page->document->scale;
+      tmp.y1 = (page->width - rectangle.x2) * page->document->scale;
+      tmp.y2 = (page->width - rectangle.x1) * page->document->scale;
       break;
     default:
       tmp.x1 = rectangle.x1 * page->document->scale;
       tmp.x2 = rectangle.x2 * page->document->scale;
-      tmp.y1 = (page->height - rectangle.y1) * page->document->scale;
-      tmp.y2 = (page->height - rectangle.y2) * page->document->scale;
+      tmp.y1 = rectangle.y1 * page->document->scale;
+      tmp.y2 = rectangle.y2 * page->document->scale;
   }
 
   return tmp;