Students' metacognitive skills and perceptions are considered important variables for high-quality learning. In this study, students' perceptions were used to identify histological threshold concepts (integrative, irreversible, transformative, and troublesome) in three health sciences curricula. A specific questionnaire was developed and validated to characterize students' perceptions of histological threshold concepts. A sample of 410 undergraduate students enrolled in the dentistry, medicine, and pharmacy degree programs participated in the study. Concepts assessed in the study were clustered to ten categories (factors) by exploratory and confirmatory factor analysis. Concepts linked to tissue organization and tissue functional states received the highest scores from students in all degree programs, suggesting that the process of learning histology requires the integration of both static concepts related to the constituent elements of tissues and dynamic concepts such as stem cells as a tissue renewal substrate, or the euplasic, proplasic and retroplasic states of tissues. The complexity of integrating static and dynamic concepts may pose a challenging barrier to the comprehension of histology. In addition, several differences were detected among the students in different degree programs. Dentistry students more often perceived morphostructural concepts as threshold concepts, whereas medical students highlighted concepts related to two-dimensional microscopic identification. Lastly, pharmacy students identified concepts related to tissue general activity as critical for the comprehension and learning of histology. The identification of threshold concepts through students' perceptions is potentially useful to improve the teaching and learning process in health sciences curricula.