BackgroundObesity is a major risk factor for obstructive sleep apnea, impaired pulmonary function and heart failure, but obesity is also associated with paradoxically low levels of serum N-terminal pro-B-type natriuretic peptide (NT-proBNP). In subjects with severe obesity undergoing weight loss treatment, we assessed the associations between changes in severity of obstructive sleep apnea, pulmonary function and serum NT-proBNP levels.MethodsOne-year non-randomized controlled clinical trial. Participants, 69.6 % women, mean (SD) age 44.6 (10.8) years and body mass index (BMI) 45.1 (5.6) kg/m2, underwent gastric bypass surgery (n = 76) or intensive lifestyle intervention (n = 63), resulting in 30 (8) % and 8 (9) % weight loss, respectively. The reference group included 30 normal weight, healthy, gender and age matched controls. Sleep recordings, arterial blood gases, pulmonary function and blood tests were assessed before and 1 year after the interventions.ResultsNT-proBNP concentrations increased significantly more after surgery than after lifestyle intervention. The post intervention values in both groups were significantly higher than in a normal weight healthy reference group. In the whole study population changes (∆) in NT-proBNP correlated significantly with changes in both BMI (r = −0.213) and apnea hypopnea index (AHI, r = −0.354). ∆NT-proBNP was, independent of age, gender and ∆BMI, associated with ∆AHI (beta −0.216, p = 0.021). ∆AHI was, independent of ∆BMI, significantly associated with changes in pO2 (beta −0.204), pCO2 (beta 0.199), forced vital capacity (beta −0.168) and forced expiratory volume first second (beta −0.160).ConclusionsGastric bypass surgery was associated with a greater increase in NT-proBNP concentrations than non-surgical weight loss treatment. Reduced AHI was, independent of weight loss, associated with increased NT-proBNP levels and improved dynamic lung volumes and daytime blood gases.Clinical Trial Registration ClinicalTrials.gov NCT00273104, retrospectively registered Jan 5, 2006 (study start Dec 2005)Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2241-x) contains supplementary material, which is available to authorized users.