The genetic basis for differential regulation of breathing is certainly multigenic. The current paper builds upon a well-established genetic model of differential breathing using inbred mouse strains. We tested the interactive effects of hypoxia and hypercapnia in two strains known for variation in hypercapnic ventilatory sensitivity (HCVS); i.e. high gain in C57BL/6J (B6) and low gain in C3H/HeJ (C3) mice. Strain differences in the magnitude and pattern of breathing were measured during normoxia (F_IO₂=0.21) and hypoxia (F_IO₂=0.10) with mild or severe hypercapnia (F_ICO₂=0.03 or 0.08) using whole body plethysmography. At each level of F_IO₂, the change in minute ventilation (V_E) from 3 to 8% CO₂ was computed, and the strain differences between B6 and C3 in HCVS were maintained. Inheritance patterns showed potentiation effects of hypoxia on HCVS (i.e. CO₂ potentiation) unique to the F1 offspring of B6 and C3 progenitors; i.e., the change in V_E from 3 to 8% CO₂ was significantly greater (P<0.01) with hypoxia relative to normoxia in F1 mice. Linkage analysis using intercross progeny (F2, n = 52) of B6 and C3 progenitors revealed two significant quantitative trait loci (QTL) associated with variable HCVS phenotypes. After normalizing for body weight, variation in V_E responses during 8% CO₂ in hypoxia was linked to mouse chromosome 1 (LOD score = 4.4) in an interval between 68 and 89 cM (i.e. between D1Mit14 and D1Mit291). The second QTL linked differences in CO₂ potentiation to mouse chromosome 5 (LOD score = 3.7) in a region between 7 and 29 cM (i.e. centered at D5Mit66). In conclusion, these results support the hypothesis that a minimum of two significant genes modulate the interactive effects of hypoxia and hypercapnia in this genetic model.