Sleep is systematically modulated by chronotype in day-workers. Therefore, investigations into how shift-work affects sleep, health, and cognition may provide more reliable insights if they consider individual circadian time (chronotype). The Munich ChronoType Questionnaire (MCTQ) is a useful tool for determining chronotype. It assesses chronotype based on sleep behavior, specifically on the local time of mid-sleep on free days corrected for sleep debt accumulated over the workweek (MSFsc). Because the original MCTQ addresses people working standard hours, we developed an extended version that accommodates shift-work (MCTQShift). We first present the validation of this new version with daily sleep logs (n = 52) and actimetry (n = 27). Next, we evaluated 371 MCTQShift entries of shift-workers (rotating through 8-h shifts starting at 0600 h, 1400 h, and 2200 h). Our results support experimental findings showing that sleep is difficult to initiate and to maintain under the constraints of shift-work. Sleep times are remarkably stable on free days (on average between midnight and 0900 h), so that chronotype of shift-workers can be assessed by means of MSF—similar to that of day-workers. Sleep times on free-days are, however, slightly influenced by the preceding shift (displacements <1 h), which are smallest after evening shifts. We therefore chose this shift-specific mid-sleep time (MSFE) to assess chronotype in shift-workers. The distribution of MSFE in our sample is identical to that of MSF in day-workers. We propose conversion algorithms for chronotyping shift-workers whose schedules do not include free days after evening shifts.