The nature of word recognition difficulties in developmental dyslexia is still a topic of controversy. We investigated the contribution of phonological processing deficits and uncertainty to the word recognition difficulties of dyslexic children by mathematical diffusion modeling of visual and auditory lexical decision data. The first study showed that poor visual lexical decision performance of reading disabled children was mainly due to a delay in the evaluation of word characteristics, suggesting impaired phonological processing. The adoption of elevated certainty criteria by the disabled readers suggests that uncertainty contributed to the visual word recognition impairments as well. The second study replicated the outcomes for visual lexical decision with formally diagnosed dyslexic children. In addition, during auditory lexical decision, dyslexics presented with reduced accuracy, which also resulted from delayed evaluation of word characteristics. Since orthographic influences are diminished during auditory lexical decision, this strengthens the phonological processing deficit account. Dyslexic children did not adopt heightened certainty criteria during auditory lexical decision, indicating that uncertainty solely impairs reading and not listening.