Microarrays provide the opportunity to measure transcription from regions of the genome without bias towards the location of known genes. This technology thus offers an important source of genomic sequence annotation that is complementary to cDNA sequencing and computational gene-finding methods. Recent "tiling" microarray experiments that assay transcription at regular intervals throughout the genome have shown evidence of large amounts of transcription outside the boundaries of known genes. This transcription is observed in polyadenylated RNA samples and appears to be derived from intergenic regions, from introns of known genes and from sequences antisense to known transcripts. In this article, we discuss different explanations for this phenomenon.