In the past decade, the advent of microarray technologies has allowed functional genomic studies of male germ cell development, resulting in the identification of genes governing various processes. A major limitation with conventional gene expression microarray is that results obtained are biased due to gene probe design. The gene probes for expression microarrays are usually represented by a small number of probes located at the 3' end of a transcript. Tiling microarrays eliminate such issue by interrogating the genome in an unbiased fashion through probes tiled across the entire genome. These arrays provide higher genomic resolution and allow the identification of novel transcripts. To reveal the complexity of the genomic landscape of developing male germ cells, we applied tiling microarray to evaluate the transcriptome in spermatogonial cells. Over 50% of all known mouse genes are expressed during testicular development. More than 47% of the transcripts are uncharacterized. The results suggested that the transcription machinery in spermaotogonial cells is more complex than previously envisioned.