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Abstract Infantile skin problems not only cause temporary pain and discomfort, but also have a long-term impact on health. Hence, the purpose of this cross-sectional study was to clarify the relationship between inflammatory cytokines and Malassezia fungal facial skin problems in infants. Ninety-six 1-month-old infants were examined. Facial skin problems and the presence of inflammatory cytokines in the forehead skin were assessed using the infant facial skin visual assessment tool (IFSAT) and the skin blotting method, respectively. Malassezia, a fungal commensal, was detected using forehead skin swabs, and its percentage in the total fungal population was analyzed. Infants with positive interleukin-8 signals were more likely to have severe facial skin problems (p = 0.006) and forehead papules (p = 0.043). No significant association between IFSAT scores and Malassezia was found, but infants with forehead dryness had a lower percentage of M. arunalokei in the total fungal population (p = 0.006). No significant association was observed between inflammatory cytokines and Malassezia in the study participants. Longitudinal studies on the development of facial skin problems in infants are warranted to investigate the involvement of interleukin-8 and devise preventive strategies in the future.