Impaired perception of consonants by poor readers is reflected in poor subcortical encoding of speech timing and harmonics. We assessed auditory brainstem representation of higher harmonics within a consonant-vowel formant transition to identify relationships between speech fine structure and reading. Responses were analyzed in three ways: a single stimulus polarity, adding responses to inverted polarities (emphasizing low harmonics), and subtracting responses to inverted polarities (emphasizing high harmonics). Poor readers had a reduced representation of higher speech harmonics for subtracted polarities and a single polarity. No group differences were found for the fundamental frequency. These findings strengthen the evidence of subcortical encoding deficits in poor readers for speech fine structure and delineate effective strategies for capturing these neural impairments in humans.