Funding was used to create and refine item response theory models of the difficulty of individual English phonemes. Elementary school students responded to digital prompts. Results indicate an increased difficulty for both complex vowels and less regular letter-sound combinations (e.g., u, v). Statistical analyses of the cross-sectional results indicated three separate types of phonemes: those with relative parity with Japanese (easier), those with irregular parity with Japanese (more difficult), and those with poor parity with Japanese (hardest). Vowel sounds not represented by common Japanese sounds comprised the largest part of the two more difficult factors, and showed the greatest difficulty across all grades tested. Results indicate the necessity to continuously re-assess sound-letter connection difficulties, both for students with reading problems and for students acquiring initial sound-letter fluency.