Common laboratory inbred mouse strains (C3H/HeJ, BALB/cByJ, C57BL/6J, A/J, JF1/Msf, PWD/PhJ) vary in pulmonary functions like lung volumes, compliance, diffusing capacity, with C3H and BALB strains versus the JF1 and PWD strains representing the two phenotypic extremes. Genome wide linkage analysis in mice by Reinhard et al. (2005) identified genetic loci with linkage to these lung function parameters. The genes Rxrb, Pdgfb, Rln1, Sod3 and Tgfbr3 are located within the chromosomal regions with highest linkage scores and thus considered to be the major candidates. In order to detect the genetic basis for the variation in lung functions among the above mentioned strains of mice, the candidate genes were analysed for strain specific variations like single nucleotide polymorphisms (SNPs) following exon-wise PCR amplification of the genomic DNA and nucleotide sequencing. To date, SNPs leading to amino acid exchanges that can essentially alter the structure, properties and functionality of the respective proteins have been detected in case of Rxrb, Pdgfb, Rln1 and Sod3. These molecular alterations are supposed to play a significant role for pulmonary functions mainly by modulating lung development. These results contribute to the novel research area of lung function genetics. Supported by NIH (HL70542) and NGFN (1GR0430)