Introduction: Variations in chronotype influence sleep quality in humans. Insufficient sleep can have adverse consequences for students' health and academic performance. The aim of our study was to measure the associations between chronotype and sleep quality in a population of 1210 students of health sciences in Morocco and Spain. Methods: The study variables were assessed using the Horne and Ostberg Morningness–Eveningness Questionnaire (MEQ) and the Pittsburgh Sleep Quality Index (PSQI). Results: This study revealed that the majority of the students belonged to the "neutral" chronotype (73.9%) and that the prevalence of poor-quality sleep was high (74.0%). Associations were found between chronotype and subjective sleep quality (p=0.006), sleep duration (p=0.005), sleep disturbances (p=0.013) and the use of sleeping medication (p=0.003). Chronotype was also associated with gender (p=0.009), country of study (p<0.001), field of study (p<0.001) and chronic health problems (p=0.001). The associations between chronotype and field of study (p<0.001 for an evening chronotype) and between chronotype and sleep disturbances (p<0.001 and p=0.026 for evening and morning chronotypes) were confirmed in the multivariate analysis. Conclusions: We have highlighted the influences of chronotype on sleep quality, which point to the need to undertake educational activities on sleep hygiene, taking chronotype into account among science students, in order to improve the mental health of future health professionals.