Hypoxia inhibits vertebrate development, but the magnitude and timing of organ-specific effects are poorly understood. Chick embryos were exposed continuously to hypoxia (15% O2) throughout Days 1-6, 6-12, 12-18 or Days 1-18 of development, followed by morphometric measurements of major organ systems. Early hypoxic exposure reduced eye mass and beak length when measured in middle development. Liver, brain, heart, kidneys, stomach, intestines and skeletal long bones were not affected by hypoxia at any developmental stage. The chorioallantoic membrane (CAM) mass was unchanged by hypoxic exposure in early or mid-development, but CAM mass on Day 18 increased strikingly (40 and 60% in late and continuous populations, respectively) in response to hypoxic exposure. The increase in CAM mass presumably enhances oxygen delivery, thus minimizing the detrimental effects of hypoxia on development and growth. Hypoxic exposure at key critical windows in development thus results in differential effects on organ development, some of which can subsequently be repaired through additional incubation (yolk mass, eye mass, beak length).