School system in which classes are scheduled 1 week in the morning and the other in the afternoon, and in which students rotate schedule every week, fosters sleep irregularity. In this study, we examined morningness-eveningness of adolescents who were involved in such schedule of school time and explored relationship between their circadian preferences and sleep characteristics. A large sample of 2287 students between the ages 11 and 18 years (52% girls) from 24 schools in Croatia was studied. The School Sleep Habits Survey was modified to enable differentiation of sleep patterns between the two school schedules and weekends. Two measures of ME were used: the Morningness-Eveningness Scale for Children (MESC) and mid-sleep time on weekends (MSFsc). Both measures showed a shift to eveningness starting between the ages 12 and 13 (MESC), or 13 and 14 (MSFsc). However, MESC demonstrated a plateau in the shift in older adolescent whereas MSFsc indicated further progress of phase delay. Significant differences in sleep timing and duration were found between three chronotype groups (Morning, Intermediate, and Evening). Generally, Evening types went to bed and woke up the latest in all situations. Their sleep duration was the shortest on school week with morning schedule. On weekends Morning types slept shorter than other two chronotype groups. On school week with afternoon schedule all chronotype groups slept close to the recommended 9 h. All three chronotype groups delayed their bedtimes and wake-up times, and extended their sleep in situations with fewer constraints on sleep timing (i.e. afternoon school schedule, and weekends versus morning school schedule). Expectedly, the evening types showed the greatest sleep irregularity. The findings of this study suggest that the Croatian school system fosters sleep irregularity, but provides more opportunity for fulfilling sleep need of all chronotype groups of adolescents. Age effects on morningness-eveningness observed in Croatian adolescent do not seem to be different from those observed in adolescents from other countries involved in a regular morning school schedule. Further studies are necessary to explore differences in the trend of shift towards eveningness found between the two measures of morningness-eveningness in this, as well as in other studies.