AbstractHypoxia at high altitude facilitates changes in ventilatory control that can lead to nocturnal periodic breathing (nPB). Here, we introduce a placebo‐controlled approach to prevent nPB by increasing inspiratory CO₂ and used it to assess whether nPB contributes to the adverse effects of hypoxia on sleep architecture. In a randomized, single‐blinded, crossover design, 12 men underwent two sojourns (three days/nights each, separated by 4 weeks) in hypobaric hypoxia corresponding to 4000 m altitude, with polysomnography during the first and third night of each sojourn. During all nights, subjects’ heads were encompassed by a canopy retaining exhaled CO₂, and CO₂ concentration in the canopy (i.e. inspiratory CO₂ concentration) was controlled by adjustment of fresh air inflow. Throughout the placebo sojourn inspiratory CO₂ was ≤0.2%, whereas throughout the other sojourn it was increased to 1.76% (IQR, 1.07%–2.44%). During the placebo sojourn, total sleep time (TST) with nPB was 54.3% (37.4%–80.8%) and 45.0% (24.5%–56.5%) during the first and the third night, respectively (P = 0.042). Increased inspiratory CO₂ reduced TST with nPB by an absolute 38.1% (28.1%–48.1%), the apnoea–hypopnoea index by 58.1/h (40.1–76.1/h), and oxygen desaturation index ≥3% by 56.0/h (38.9.1–73.2/h) (all P < 0.001), whereas it increased the mean arterial oxygen saturation in TST by 2.0% (0.4%–3.5%, P = 0.035). Increased inspiratory CO₂ slightly increased the percentage of N3 sleep during the third night (P = 0.045), without other effects on sleep architecture. Increasing inspiratory CO₂ effectively prevented hypoxia‐induced nPB without affecting sleep macro‐architecture, indicating that nPB does not explain the sleep deterioration commonly observed at high altitudes. imageKey points Periodic breathing is common during sleep at high altitude, and it is unclear how this affects sleep architecture. We developed a placebo‐controlled approach to prevent nocturnal periodic breathing (nPB) with inspiratory CO₂ administration and used it to assess the effects of nPB on sleep in hypobaric hypoxia. Nocturnal periodic breathing was effectively mitigated by an increased inspiratory CO₂ fraction in a blinded manner. Prevention of nPB did not lead to relevant changes in sleep architecture in hypobaric hypoxia. We conclude that nPB does not explain the deterioration in sleep architecture commonly observed at high altitude.