Academic stress is a problem that affects students due to a number of factors that are considered stressors. These include academic overload and completion of assignments and exams, exacerbated by such external conditions as family, social and economic problems. Together, these can affect emotional and physical health, which may lead in the long term to developing a number of pathologies, given the alteration of immunological homoeostasis with which they are related. Objective: To evaluate the effect of academic stress on the production of cytokines IL‐6, TNF‐α, IL‐1β and IL‐10 in Morphology students in the Faculty of Health Sciences of the Universidad del Cauca during an academic period. Methodology: A descriptive longitudinal study was carried out with a population of 78 students studying Morphology, among the subjects with the highest academic load in the Physiotherapy, Medicine, Nursing and Phonoaudiology programs in the Faculty. Academic stress was assessed in the students by applying the Academic Stress Questionnaire (ASQ), and through quantification of the IL‐6, TNF‐α, IL‐1β and IL‐10 cytokines using the ELISA (Enzyme‐linked immunosorbent assay) technique in three “moments” of the academic semester: Moment 1: beginning of the academic semester; Moment 2: week of evaluations of 70% of the semester; Moment 3: week of final exams. Results: The students perceived stress as “normal” at Moment 1, while at Moments 2 and 3 it was perceived as "quite a lot", with percentages of 48.7% and 50%, respectively. The predominant stressors were: “methodological deficiencies”, “academic overload”, and “exams”, for the three moments of the study. “Physical exhaustion” was the most prevalent stress response at all three moments, followed by “irascible behaviour” (Moment 2 and 3), and “sleep disturbances” (Moment 3). To cope with the stress, the students resorted mainly to "planning and management of personal resources" in the three moments of the study. A progressive increase in the pro‐inflammatory cytokines IL‐6 and TNF‐α and a decrease in IL‐10 were observed at all three moments. A correlation was found between some questions belonging to the "methodological deficiencies", "beliefs about performance", "sleep disturbances", "physical exhaustion" and "irascible behaviour" dimensions with IL‐6, IL‐1β, TNF‐α and IL. −10. Conclusion: The morphology students suffer increased stress indicators (perceived stress and pro‐inflammatory cytokines) throughout the academic period. The “methodological deficiencies”, “academic overload” and “exams” stressors, together with “physical exhaustion”, “sleep disturbances” and “irascible behaviour”, possibly influence the production of the IL‐6, TNF‐α and IL‐10 cytokines.