During the years 2014–2016 the University of Salento performed the “Impact of Air Quality on Health of Residents in the Municipalities of Cutrofiano, Galatina, Sogliano Cavour, Soleto and Sternatia” (IMP.AIR) study, an epidemiological-molecular research project aiming to evaluate early DNA damage in children living in an area of Salento with high incidence of lung cancer among the male population. One hundred and twenty-two children aged 6–8 years attending primary school were enrolled and the frequency of micronucleated cells (MNC) in oral mucosa was evaluated. In addition, a questionnaire was administered to parents to obtain information about personal data, anthropometric characteristics and lifestyles (physical activity, food habits, family context) of the children and perform a multivariate analysis to detect any factors associated with MNC occurrence. Data on airborne pollutants detected in the study area were acquired by the Regional Agency for the Environmental Protection. The presence of MNC was highlighted in about 42% of children with a mean MNC frequency of 0.49‰. The frequency of MNC was associated to obesity, consumption of red or processed meat and having a mother who smokes. Moreover, the prevalence of biomarkers was higher than in another area of Salento not included in the cluster area.