Recent research in dyslexia postulates that imprecise representations of phonemes are linked to basic auditory deficits in temporal sampling. Evidence comes from adult readers with dyslexia demonstrating deficits in auditory sampling at several rates of the speech signal including the phoneme rate (>40 Hz). It remains unknown whether such deficits are present in infancy, especially during the “sensitive period” for native phoneme learning (6–12 months). We examined auditory sampling in infants at risk for dyslexia across the period of native phoneme learning. Using magnetoencephalography, we recorded auditory steady-state responses (ASSRs) to white noise that was amplitude-modulated at frequency rates relevant to speech processing in 6- and 12-month-old at-risk and typically developing (TD) infants. Our results show that the two groups differed in hemisphere involvement of ASSRs at the phoneme rate (50–80 Hz): TD infants showed a shift from right-to-left hemisphere processing from 6 to 12 months, whereas at-risk infants showed stronger right-hemisphere processing at 12 than 6 months. This measure predicted words understood at 13 months. Risk for dyslexia is associated with auditory sampling deficits throughout the sensitive period. These deficits may affect future language acquisition.