To examine sleep patterns of adolescents attending school on alternating morning and afternoon schedules and to explore the contribution of sleep characteristics on the afternoon schedule to prediction of adolescents' daytime functioning.The Croatian adaptation of the School Sleep Habits Survey for a two-shift school system was completed by 2033 students (11-18 years old, 54% females) whose school start times alternated weekly between 08:00 and 14:00.All age groups of adolescents reported delayed sleep when on the school week with an afternoon schedule as compared to a morning schedule. The average delay of bedtime was 36 minutes, and delay of wake-up time 121 minutes, which resulted in average sleep durations from 9.80h in 11-year olds to 8.39h in 18-year olds. Having more delayed wake-up times on the afternoon schedule predicted more substance use and poorer grades. Having more delayed bedtimes predicted poorer grades, but also predicted less depressed mood. Obtaining relatively longer sleep on afternoon schedule predicted lower sleepiness, less depressed mood and less frequent substance use.The afternoon school start time enables sleep duration that is in line with adolescent sleep biology and contributes positively to daytime functioning. In many cases a large delay in wake-up time is observed. At least part of that delay is not associated with adolescents' circadian biology and contributes negatively to some indices of their daytime functioning. Further research of factors associated with extreme delays of sleep and/or interventions that could limit extreme sleep irregularity is required.