This paper studies the perception of Estonian duration-based phonological oppositions by native Estonians and non-native speakers with Russian-language background. The short/long category boundary was examined by varying the duration of a vowel in three contexts involving isolated vowels (V vs. VV), one-syllable nonsense words (CVC vs. CVVC), and two-syllable real words (CVCV vs. CVVCV). Since vowel duration serves to distinguish lexical minimal pairs in Estonian but not in Russian, L1 and L2 subjects are expected to employ different perceptual strategies in a short/long categorization task. In particular, location and width of category boundaries as well as consistency of categorization are likely to vary between the groups. The results showed that L2 subjects were quite successful in distinguishing the Estonian short/long categories despite the non-categorical use of the duration cue in their native language. As a rule, the L2 subjects demonstrated (1) category boundaries at longer durations, (2) larger width of category boundaries, and (3) lower consistency of responses compared to those of the L1 group. The perceptual strategies of L2 subjects might be based on the continuous auditory perception of the salient duration cue, or on the variable duration patterns associated with word stress in their L1, or on a combination of both strategies.