This study examined how differently native speakers of Japanese discriminated between the American English vowels /e/ and /ae/ in /CVp/ syllables with 20 different initial consonants, and how the differing discrimination was related to the formant changes throughout the vowels in comparison with the Japanese vowels /e/ and /a/. A perceptual test and formant analyses of the English and Japanese vowels were conducted. The results showed that there were significant differences in discrimination across the consonantal contexts: the discrimination of /e/ was significantly poorer when the initial consonant was /dg/, /g/, /ch/, /m/ or /th/ (voiceless), and that of /ae/, when it was /sh/, /h/ or /t/. It was found that the poorer discrimination was more related to the smaller formant ratios (F2/F1) and the higher F1 frequency in the latter part of /e/, and to the larger formant ratios and the lower F1 frequency in the latter part of /ae/. The changing of formant patterns throughout the two English vowels could be attributed to the poorer discrimination in the particular consonantal contexts.