Ultra-selfish genes increase in frequency in a population despite the harm they inflict on their host. The spread of both ultra-selfish genes and their suppressors is evidence of conflicts between genes within an individual for transmission into the next generation. Here I synthesize a body of past work, and argue that intragenomic conflict might be an important evolutionary force. I discuss the evolutionary history of cytoplasmic genes as an illustration. I first consider the evolution of sex. Recent evidence suggests that the initial evolution of sex might have been driven by an ultra-selfish gene. The existence of sex in turn creates a series of new conflicts which may explain the existence of sexes and uniparental inheritance of cytoplasmic genes. Uniparental inheritance of cytoplasmic genes sets up a new set of conflicts over the sex ratio, which in turn may influence the evolution of sex determining systems, sex allocation systems and post-zygotic isolating mechanisms.