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The interactions between attention and stimulus encoding in infancy were examined using heart rate (HR) and visual habituation measures. At 3, 6, and 9 months of age, infants (N = 119) were habituated to an adult face; longest look (LL) duration was measured as an indicator of encoding speed. Three groups were formed based on LL change from 3 to 9 months: Large Decrease, Small Decrease, and Increase. Using concurrent electrocardiograph recordings, attention was measured through the percentage of looking time in orienting, sustained attention, and attention termination. We partially replicated previous findings regarding developmental patterns of attention in these three groups, notably that these patterns were different for the Increase group. Looks away from the stimulus were also assessed in each attentional phase and, as predicted, HR acceleration phases showed less visual engagement than HR deceleration phases. We also found anomalous behavior for the LL Increase group. In general, this small but distinct group showed similarities at 3 months to the presumably more mature behavior of typical 9 month olds, but by 9 months, they behaved more like typical 3 month olds regarding some, but not all, cognitive measures. These results are discussed in the context of the development of endogenous attention.