BACKGROUND: One of every five children and adolescents in the European Union suffers from behavioural, and emotional disturbances. OBJECTIVES: To compare factors associated with the quality of life and mental health of immigrant and Spanish children aged 4-14years both during the years 2006 and 2012 and to evaluate changes over this time period. DESIGN AND METHODS: An epidemiologic age and sex matched case-control study (1:2) was conducted. The study group were 677 immigrant children and 1354 matched Spanish children (controls). This study was conducted using data obtained from the Spanish National Health Surveys done in 2006 and 2012. We used the Strengths and Difficulties Questionnaire to obtain the score for variables derived from mental health and the Kidscreen-10 questionnaire to score the Health-Related Quality of Life. RESULTS: Spanish girls scored higher in conduct problems (2.04+/-0.1) and better in problems with peers (1.21+/-0.08) regarding immigrant girls (1.82+/-0.12-1.92+/-0.13 respectively). Concerning total scores, immigrant children obtained significantly lower scores in quality of life (81.29+/-0.76) and in problems with peers (2.04+/-0.09) than their matched Spanish children (84.4+/-0.45 and 1.26+/-0.06) in 2006. Immigrant children had lower total scores in prosocial behaviour (8.62+/-0.11) compared to the matched Spanish children (8.92+/-0.06) in 2012. The total average scores of immigrant children in terms of quality of life, emotional symptoms, behavioural problems, hyperactivity and problems with peers were significantly better in 2012 (86.58; 1.84; 1.46; 3.77 and 1.48 respectively) than in 2006 (81.29; 2.15; 1.90; 4.58 and2.04). CONCLUSIONS: Immigrant children had a poorer quality of life and mental health than matched Spanish children in 2006.