The aim of this study was to compare differences in morphological effects following two regimens of simulated chronic intermittent hypoxia (4600 m) during 12 months, compared to chronic hypoxia and normoxia. Male Wistar rats were randomly assigned to four groups: Chronic intermittent hypoxia (CIH) 2 × 2 (2 days hypoxia, 2 days normoxia, n = 50), CIH4 × 4 (4 days hypoxia, 4 days normoxia, n =50), chronic hypoxia (CH) (permanent, n = 28) and control (NX) (normoxia, n = 24). Hypoxia was simulated in a hypobaric chamber (428 torr). The following parameters were assessed: ventricle wall thickness, presence of congestion, edema, hemorrhage, thrombosis, necrosis, and renal casts. In general, mortality was significantly associated with heart congestion, pulmonary edema, pulmonary hemorrhage, and liver necrosis. Intermittent as well as chronic exposure produced a common pattern of manifestations in all organs, with varying severity and time of occurrence. Right ventricle hypertrophy was observed in CIH2 × 2 and CIH4 × 4 but attained lower values than in CH. Further, the coefficient of right ventricular wall thickness rose markedly dependent upon exposure duration. Renal casts and thrombosis were also shown to be the signs of hypoxic damage. Morphological effects in intermittent hypoxia resembled an intermediate severity position compared to CH and tended to occur later, indicating that a shorter regimen seemed to be less harmful. © 2007 Taylor & Francis.