The bacterial aspects of the events occurring during the first days of lung colonization by Pseudomonas aeruginosa are still unknown. The aim of this study was to develop a real time RT-PCR method for the direct quantification of the transcripts of three P. aeruginosa virulence genes: exoS, lasI and algD, during the first seven days of a rat lung infection. Our results document differences in bacterial gene expression throughout P. aeruginosa infection. ExoS transcripts levels were very high in the first days of infection, but a significant decrease was then progressively observed. Transcription of algD occurred on the 4th day and increased regularly over time suggesting a balance in the transcription of exoS and algD. The strong expression of exoS during the first 3 days was correlated to 29% of mortality among infected rats. On the contrary, the increase of algD expression after this period was associated to the development of a chronic infection with no further mortality. LasI transcription remained more constant throughout the infection.