Oscillations in oxygen uptake (V(O2)) and carbon dioxide production (V(CO2)) in patients with chronic heart failure differ in amplitude and phase from the oscillations in ventilation (periodic breathing, PB), leading some to doubt whether they result from PB. We applied Fourier transforms to a pulmonary gas exchange model to quantify the effects of fluctuations in alveolar ventilation (V(A)). We found that PB causes oscillations in V(O2) and V(CO2), but their amplitude and phase are complex, and vary with workload. At low workloads, the relative oscillations in V(O2) and V(CO2) closely mirror the relative oscillations in V(A). But at high workloads, the metabolic oscillations are attenuated (V(O2) most severely), and the V(O2) peaks precede the ventilatory peaks significantly. This study also explains why normal controls simulating PB at higher workloads fail to reproduce the V(O2) and V(CO2) oscillations seen in spontaneous PB of heart failure.