Over the last several years the search for functional genomic elements by exploiting motif over-representation became increasingly popular. However, about half of the human genome is repetitive, and that is also the case with most higher eukaryotes. In this study we have shown that in addition to these known repeats, human sequences feature many short over-represented motifs, and that their frequency varies only slightly between random repeat-masked sequences and regions located immediately upstream of the known genes. Most of our study has been performed on the ENCODE sequences, which comprise about 1% of the human genome.