Here we measured adults’ and 9-month-old German-learning infants’ pupil size while they were familiarized with an artificial speech stream without pauses in which prosodic cues and statistical cues were pitted against each other. We found that adults’ changes in pupil size synchronized with the occurrence of prosodic words during the familiarization. Nine-month-old infants showed variability in temporal alignment of the pupillary changes at word frequency that was predictive of the cues they used for segmentation. A follow-up language questionnaire at 40 months suggests that infants who entrained to prosodic words performed better on the vocabulary task and those infants who relied more on statistical cues performed better on grammatical tasks. Together these results suggest that at this age there is variability in word segmentation and that the different cues, statistics and prosody, may serve different roles in speech segmentation in infancy.