Background. Malnutrition has been consistently associated with caries in primary teeth, although an effect on permanent teeth has not been established because of the few longitudinal studies. Aim. To explore the association between stunting and caries increment in permanent teeth over 3.5years. Design. In 2003, 121 children aged 7-9years were randomly selected from nine underserved communities in Lima (Peru). Parents provided demographic information and a food diary for their children. Clinical examinations included assessments of height, weight, oral hygiene, and dental caries. Stunting was defined using the 2000 CDC and 2007 WHO standards. In 2006, 83 children were re-examined, and the 3.5-year net DMFS increment was calculated. The association between stunting and net DMFS increment was assessed using negative binomial regression. Results. Stunting was related to net DMFS increment after adjustment for sex and age, oral hygiene, sugary snacks between meals, and caries experience in primary and permanent teeth. Consistent results were found when using either the 2000 CDC (incidence rate ratio: 1.61; 95%CI: 1.07, 2.44) or 2007 WHO standards (IRR: 1.79; 95%CI: 1.28, 2.51). Conclusion. Stunting was a significant risk factor for caries increment in permanent teeth over a 3.5-year period, independent of other well-known risk factors for caries development. © 2012 The Authors. International Journal of Paediatric Dentistry. © 2012 BSPD, IAPD and Blackwell Publishing Ltd.