To further elucidate the characteristics and potential functions of non-coding region of certain genes, we here systematically examined alternative promoter regions and repeated elements in non-coding regulatory regions of human tissue-specific genes. The results demonstrated that the different types of tissue-specific gene show distinct characteristics, such as the type of alternative promoters, CpG islands, initiating intervallic dinucleotides, and repeat elements. Surprisingly, 74.8% of selected genes contain more than one putative alternative promoter (PAP), and about 92.11% of signal receptors (membrane-bound) possess PAPs. Moreover, a specific PAP type (GC-GC type: both the downstream (?300) and the upstream (-700) regions of transcription start sites are GC-rich) is dominant in human tissue-specific genes and the tissue-specific transcription factors have significantly higher proportion of GC-GC type PAPs. Notably, our data indicated that more than 80% of PAPs are CpG-poor in the considered genes. Furthermore, our findings revealed an inverse tendency between transposable elements and other repeated elements in the 50 flanking regions. These results seem to imply that the distinct alternative promoters and repeated elements may contribute to the regulation and divergence of human tissue-specific genes.