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My quick testing, using ArcGIS 10.2.2 for Desktop on Windows 7 SP1, indicates that Intersect is faster than Spatial Join. This test, run from IDLE: import arcpy,time if not arcpy.Exists(r"C:\temp\test.gdb"): arcpy.CreateFileGDB_management(r"C:\temp","test.gdb") if arcpy.Exists(r"C:\temp\test.gdb\fnPoly100"): ...

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