import arcpy
import ctypes

inFile = arcpy.GetParameterAsText(0)
arcpy.AddMessage("nInput file: {0}n".format(inFile))

# Yes/No mbox = 4, return code Yes = 6, return code No = 7
mBox = ctypes.windll.user32.MessageBoxW
result = mBox(None, u"Just checking...", u"File Check", 4)

if result == 6:
    arcpy.AddMessage("User pressed Yesn")
elif result == 7:
    arcpy.AddMessage("User pressed Non")
else:
    arcpy.AddMessage("Unknown return coden")

arcpy.AddMessage("Complete.n")