Pseudogenes have long been considered nonfunctional elements. However, recent studies have shown they can potentially regulate the expression of protein-coding genes. Capitalizing on available functional-genomics data and the finished annotation of human, worm, and fly, we compared the pseudogene complements across the three phyla. We found that in contrast to protein-coding genes, pseudogenes are highly lineage specific, reflecting genome history more so than the conservation of essential biological functions. Specifically, the human pseudogene complement reflects a massive burst of retrotranspositional activity at the dawn of the primates, whereas the worm's and fly's repertoire reflects a history of deactivated duplications. However, we also observe that pseudogenes across the three phyla have a consistent level of partial activity, with ∼15% being transcribed.