BACKGROUND: Adolescence has been documented as the peak age of onset for mental health perturbations, clinical disorders and unsubstantiated health complaints. The present study attempted to investigate associations between multiple, recurrent subjective health complaints (SHC) with emotional/behavioural difficulties, as measured by the Strengths and Difficulties Questionnaire scale (SDQ), among Greek adolescents. METHODS: Questionnaires were administered in a large, nation-wide, random, school-based sample of Greek adolescents, aged 12-18 years. Data from 1170 participants were analyzed. Adolescents with multiple, recurrent SHC were compared in terms of their emotional/behavioural difficulties to their peers with lower levels of health complaints. SDQ scales were separately investigated for their associations with multiple, recurrent SHC, after adjustment for gender, age and socioeconomic status (ses). Further analysis included multiple logistic regression models with multiple, recurrent SHC as the dependent variable and gender, age, ses and SDQ Total difficulties score as independent factors. Potential gender and age interactions were also explored. RESULTS: Almost half of the study participants reported multiple, recurrent SHC. Adolescents with multiple, recurrent SHC had higher scores on all SDQ scales, except from the Prosocial behavior scale, compared to their peers with lower levels of health complaints. Emotional Symptoms, Conduct Problems, Hyperactivity/Inattention and Peer Problems were associated with greater likelihood of having multiple, recurrent SHC, after adjustment for gender, age and ses. The multiple logistic regression models revealed that older adolescents and girls, as well as those with increased Total difficulties score had an increased risk for multiple, recurrent SHC reporting. No significant interaction between SDQ scales and gender or age was found. CONCLUSIONS: Our study highlights the magnitude of psychological burden among adolescents experiencing multiple, recurrent SHC. Professionals in school and clinical settings should be cautious for impaired emotional/behavioural functioning when assessing adolescents with multiple, recurrent SHC, so as early identification of at-risk individuals and timely, appropriate referrals are facilitated.