Acoustic characteristics including vowel duration for the same speech sound may vary among individual speakers. The presented study reports that the influence of variability in physical duration of a vowel on speech perception differs depending on the phonological system of the language. Ten native speakers of each of three languages, namely Japanese (mora-time), French (syllable-time) and English (stress-timed) were employed. Ten sets of V[inf 1]CuCV[inf 3] (V[inf 1],V[inf 3]=/= [u]) sequences in which the duration of [u] was varied into six degrees (from full utterance to 0 pitch period of [u], where the steady state of [u] was reduced by two pitch periods) were created. The subjects were asked to judge whether each stimulus contained the interconsonantal [u]. For English and French speakers, the frequency of the judgments in which the [u] vowel was reported corresponded to the number of the pitch periods, whereas Japanese speakers consistently reported [u] even when its pitch periods were (almost) completely removed. The results can be explained by the fact that VCCV and VCuCV do not make a linguistic contrast in the Japanese phonological system, in which a consonant cluster is illegal and [u] is always epenthesized. These results thus suggest that perception of vowels varied in physical duration may be strongly influenced by the phonological system of the language that the listener employs.