Previous studies from oligonucleotides in the ribosomal protein (RP) genes of the yeast and fruitfly indicated that the potential transcriptional regulatory sites are located in the introns of the genes. The transcriptional regulatory sites in introns are still poorly understood. To explore the functional significance of transcriptional regulation of introns, we extracted over-represented oligonucleotides (also known as motifs) in the first introns of the human and mouse ribosomal protein genes by statistical comparative analysis, and found that over 85% of these oligonucleotides were consistent with the known transcriptional factor binding sites, which might be potential transcriptional regulatory elements. By analyzing the base compositions of these elements, we found that a majority (>95%) of the detected motifs were rich in C and G and only a few of them were rich in A and T. Moreover, the oligonucleotides were close to the 5'-ends of the first introns (the distances between the motifs and the transcriptional start sites or upstream regions of genes are short). We speculated that the properties of over-represented motifs in the first introns might be associated with the transcriptional control.