Ventilatory and cardiac responses to changing inhaled gas fractions are notoriously variable within individuals. Such variation can confound clinical diagnoses and hypotheses about human adaptation. In this study we use a cardiac (HHR) and a ventilatory (HVR) measure of physiological sensitivity to an experimentally manipulated oxygen concentration (8% O₂), to compare variation (a) within and between individuals, (b) within and between days and (c) within and between physiological parameters. To explore the sources of variation, we use the coefficient of variation (CV, %), repeatability (R, intra-class correlation coefficient, %) and repeated-measures analyses of variance. Both the HVR and the HHR are significantly repeatable (HVR: R = 0.76–0.92; HHR: R = 0.35–0.76) and equally variable within and between days. Its high R suggests that the HVR displays greater between-individual variation relative to within-individual variation than does the HHR. The HVR is thus a more reliable measure of physiological sensitivity to hypoxia than is the HHR. We suggest how these results may inform experimental design, and suggest how to avoid stochastic and experimental artefacts when investigating ventilatory and cardiac physiological responses to hypoxia.