The study investigated the dynamic relation between contingency learning and heart rate with risk and non-risk babies 5- to 10-months-old. Four groups were compared in a two contingency treatments (contingent, yoked) × two risk status design. Concurrent heart rate was monitored during three phases of a contingency learning task (baseline, contingency/stimulation, extinction) and analysis focused on phase transitions. Non-risk babies presented with contingent stimulation showed an immediate increase in cardiac rate associated with a subsequent response increase to the contingency. Risk infants presented with contingent stimulation showed delayed cardiac reactivity accompanied by a smaller response increase to the contingency. Yoked controls decreased responding in the contingent period with no significant changes in cardiac reactivity at phase transitions. The findings of the study are discussed in relation to individual differences in physiological regulation and to differential sensitization in a contingency learning task.