The purpose of the present study was to investigate whether NK cells from resistant C3H/HeN mice and susceptible BALB/c mice showed different release of cytokines and expression of surface molecules during chronic P. aeruginosa lung infection using alginate-embedded P. aeruginosa mimicking the infection in cystic fibrosis. Lung cell suspensions were depleted of lymphocytes by magnetic cell sorting. The concentrations of IFN-gamma, IL-1beta and GM-CSF were estimated by ELISA at day 1 and 2 after infection. Non-infected mice were used as controls. Flow cytometry was used to estimate the surface expression of the LFA-1 and Fc receptors on NK cells. At day 2, IFN-gamma levels increased in C3H/HeN mice but decreased in BALB/c mice. The GM-CSF levels increased only in the C3H/HeN mice at day 1 and 2. Surface expression of LFA-1 on the NK cells was higher in C3H/HeN mice at day 1 and 2. In contrast, the expression of Fc receptors was significantly lower on NK cells in C3H/HeN mice at day 1 and 2. In conclusion, the present results show phenotypic differences in NK cells in the two mice strains in chronic P. aeruginosa lung infection, indicating different modulating effects in the Th1/Th2 balance.