Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level through a variety of biological mechanisms, such as transcription interference, RNA masking, dsRNA-dependent mechanisms, and chromatin remodelling (modification). We speculated that both of sense and antisense transcripts may be sliced to form small RNAs, which is also an important mechanism for NATs to regulate gene expression, such as rasiRNAs in "ping-pong". Experimental and computational analyses have demonstrated the wide-spread occurrence of NATs in a wide range of species. Here, we reviewed the current understanding of NATs function and its mechanistic basis. We hypothesized that the regulation of antisense transcription and small RNAs were derived from NATs.