Mutations in the gene for adenosine triphosphate-binding cassette transporter subfamily A member 3 (ABCA3) have been reported in infants and children with surfactant deficiency and interstitial lung disease. We report a case of siblings found to be compound heterozygotes for two novel ABCA3 gene mutations but developing very different course of lung disease. The index case is a baby girl with severe interstitial lung disease that manifested on the first days of life. Her 4-year-old brother carrying the same mutations has no signs of lung disease so far. Our findings suggest the contribution of other genetic, epigenetic and environmental factors to discordant phenotype observed in patients carrying the same mutations in the ABCA3 gene. The clinical course of the index case suggests benefit of combined medical therapy in treating infants with ABCA3 deficiency.