Whereas natural acoustic variation in speech does not compromise phoneme discrimination in healthy adults, it was hypothesized to be a challenge for developmental dyslexics. We investigated dyslexics' neural and perceptual discrimination of native language phonemes during acoustic variation. Dyslexics and non-dyslexics heard /æ/ and /i/ phonemes in a context with fo variation and then in a context without it. Mismatch negativity (MMN) and P3a responses to phoneme changes were recorded with electroencephalogram to compare groups during ignore and attentive listening. Perceptual phoneme discrimination in the variable context was evaluated with hit-ratios and reaction times. MMN/N2bs were diminished in dyslexics in the variable context. Hit-ratios were smaller in dyslexics than controls. MMNs did not differ between groups in the context without variation. These results suggest that even distinctive vowels are challenging to discriminate for dyslexics when the context resembles natural variability of speech. This most likely reflects poor categorical perception of phonemes in dyslexics. Difficulties to detect linguistically relevant invariant information during acoustic variation in speech may contribute to dyslexics' deficits in forming native language phoneme representations during infancy. Future studies should acknowledge that simple experimental paradigms with repetitive stimuli can be insensitive to dyslexics' speech processing deficits.