Studies in humans indicate genetic effects on the ventilatory response to hypoxia, but the site of these effects is unknown. The present study explores the question of whether there are genetically directed effects on the intrinsic hypoxic chemosensitivity of the carotid body. The approach was to study these responses in two inbred rat strains [spontaneously hypertensive rats (SHR) and Fischer 344 (F-344)] and to measure in vivo carotid chemosensitivity as the change in carotid sinus nerve (CSN) activity during progressive, isocapnic hypoxia and the isolated, in vitro responses of excised superfused carotid bodies, loaded with the fluorimetric indicator fura 2, measured as the cytosolic calcium response to moderate hypoxia (PO₂ = 55 mmHg). CSN responses in F-344 rats (n = 12) were uniformly low, with a shape parameter A of 13.8 ± 6.59 (SE), whereas responses in SHR (n = 15) were sevenfold higher (108 ± 24.1; P < 0.002) and showed greater variation. In vitro, intracellular calcium responses of superfused carotid bodies estimated from the fluorimetric ratio (340/380 nm) showed a greater peak increase during hypoxia in carotid bodies from SHR (140 ± 4.7%) than from F-344 rats (114 6.0%; P < 0.01). Our results indicate strain-related differences in hypoxic chemosensitivity that are intrinsic to the carotid body and that could mediate genetic effects on ventilatory responsiveness to hypoxia.