Evidence suggests that energy-protein malnutrition is associated with impaired growth and development of facial bones. The objective of this study was to investigate the association between nutritional status and reduced space for dental eruption (crowding) in permanent dentition. A cross-sectional study with probabilistic sampling design was used. We evaluated 2,060 students aged 12 to 15 years enrolled in schools in the northeast of Brazil. Crowding was defined according to World Health Organization (WHO) as misalignment of teeth due to lack of space for them to erupt in the correct position. Nutritional status was evaluated by means of body mass index and height-for-age, using the WHO’s reference curves. Parents and adolescents responded to a questionnaire about demographic, socioeconomic, biological and behavioral characteristics. The associations were estimated by odds ratio (OR) in multivariate logistic regression analysis (alpha = 0.05). Confounding and effect-modification were taken into account. An association between low height-for-age (z-score < –1SD) and crowding was only observed in adolescents with a prolonged history of mouth breathing (OR = 3.1). No association was observed between underweight and crowding. Malnutrition is related to crowding in permanent dentition among mouth-breathing adolescents. Policy actions aimed at reducing low height-for-age and unhealthy oral habits are strongly recommended. However, further studies are needed to increase the consistency of these findings and improve understanding of the subject.