Five cases were found with sequence variation in the primer binding region of the highly polymorphic STR system SE33 used in the German genetic database. This variation can produce homozygote mistyping because of failed primer binding. We calculated a variation rate of 0.0022 (0.0006-0.0056) that could lead to complications in database matching. To avoid errors in individual genetic characterisation for SE33 as described here, it is suggested that two different primer pairs should be used.