Pseudomonas aeruginosa is an opportunistic pathogen capable of transition from an environmental lifestyle to a host-associated lifestyle, as exemplified in the life-long airway infection of cystic fibrosis (CF) patients. Long-term infection is associated with extensive genetic adaptation of P. aeruginosa towards the CF airway environment generating variants with markedly altered phenotypes. Gaining insight into this adaptation process has great clinical relevance but simultaneously has the potential to increase our understanding of bacterial adaptation to a host environment. This has been the framework upon which this thesis is based. Early P. aeruginosa colonization of the CF airways is the period in which the outcome of infection is determined, i.e. if the bacteria are eventually eradicated or persist. In three patient cases the evolutionary events from initiation of infection were explored to unravel the early adaptive processes possibly securing bacterial persistence. In this early stage, clinical isolates displayed few adaptive events however these included phenotypes often observed in late chronic infection isolates including the conversion to a mucoid phenotype and increased antibiotic resistance. Detailed characterization of the mucoid phenotype revealed profound pleiotropic effects such as reduction of virulence factors and the Rhl quorum sensing system. Hence the mucoid phenotype in itself encompasses many of the traits associated with chronic infection isolates. In many CF patients intermittent colonization with P. aeruginosa is characterized by the recurrent detection of the same genotype with several months apart. Comparing patient sinus and lung isolates it was found that for some patients the paranasal sinuses constitute an important niche for P. aeruginosa during intermittent colonization. In fact, evolution within the sinus population gives rise to variants known to be adaptive to the CF lung environment including mucoid, antibiotic resistant and small colony variants. The likely downwards direction of migration between sinuses and lower airways at this stage suggests that the paranasal sinus population in these patients has the potential for seeding the lungs with pre-adapted variants and thus increase the risk of progression to chronic lung infection. Long-term infection of P. aeruginosa in CF patients can be compared to the early stage of host-restriction adaptation. One example of CF long-term infection is the dominant clone, the DK2 clone type, infecting CF patients at the Copenhagen CF clinic for more than 35 years. Characterization of the genome evolution of DK2 isolates during host-adaptation revealed substantial genome reduction; in one isolate 8 % of the genome was deleted. Thus large portions of the P. aeruginosa genome is dispensable for proliferation within the CF lung. The deletions were mediated by illegitimate and homologous recombination but were not insertion sequence (IS) element mediated as previously proposed for early stage host adaptation. The putative entry of a prophage in one isolate was the only sign of DNA uptake during infection revealing little importance of horizontal gene transfer (HGT) in the adaptation towards the CF lung and further demonstrating the general signal of loss of function compared to gain of function during adaptation to the CF lung. The transition of P. aeruginosa from its natural aquatic and terrestrial habitats into the very different CF lung environment containing multiple stresses usually not encountered by the bacteria should pose a number of challenges. Yet, P. aeruginosa displays an inherent capability for successful colonization of the CF lung with persistence seemingly mediated by only a few adaptive events.