Background: Symptoms of sleep apnea are markedly increased in children exposed to smoke from biomass fuels and are reduced by kitchen stoves that improve indoor biomass pollution. However, the impact of adherence to the use of improved stoves has not been critically examined. Methods: Sleep-related symptom questionnaires were obtained from children <15 years of age in 56 families residing in the communities of Lliupapuquio, Andahuaylas province in Peru before and 2 years after installation of less-polluting Inkawasi cooking stoves. Results: 82 children with lifetime exposures to indoor fuel pollution were included. When compared to those alternating between both types of stoves or those using traditional stoves only, those children who exclusively used Inkawasi cooking stoves showed significant improvements in sleep and respiratory related symptoms, but some minor albeit significant improvements occurred when both stoves were concomitantly used. Conclusions: Improvements in respiratory and sleep-related symptoms associated with elevated indoor biomass pollution occur only following implementation and exclusive utilization of improved kitchen stoves. © 2014 Accinelli et al.; licensee BioMed Central Ltd.