The aim of this study was to test the hypothesis that atopic conditions at 15/16 years of age affect both internalized and externalized mental health problems 3 years later. Combined school and postal survey was conducted in urban and rural settings. A total of 3,674 adolescents (70.1% response rate) were followed at two time points and interviewed with similar questionnaires at baseline and follow-up. Hopkins Symptoms Checklist (HSCL-10) was used to assess internalized problems, and two subscales (conduct problems and hyperactivity) from the Strength and Difficulties Questionnaire to measure externalized mental health problems. The atopic conditions investigated were asthma, hay fever and eczema by asking the adolescents whether these conditions were present or not. There was an increase in the prevalence of internalized mental health problems from about 17-25% and a decrease in externalized mental health problems and number of atopic conditions in the follow-up period. Of the atopic conditions, hay fever was most prevalent with about 34% at 15 years of age and 20% at 18. The asthma prevalence was at 10 and 5% and eczema at 25 and 10%, respectively. Internalized mental health problems among girls were significantly associated with atopic conditions 3 years earlier, also after controlling for confounding variables. To live with atopic conditions seem to affect the mood and level of anxiety among adolescent girls. This should be kept in mind by health professionals treating young girls with atopic conditions.