BACKGROUND: Severe mood dysregulation is common in childhood and can be highly impairing. The Dysregulation Profile (DP) can be considered as a broader phenotype of emotional dysregulation, including affect, cognition and behaviour. Since mood dysregulation may persist, but differently in boys and girls, the gender associated course needs to be considered longitudinally to gain a better insight in order to support the children more adequately. This study is focusing on gender associated subgroup trajectories of the Strengths and Difficulties Questionnaire-Dysregulation Profile (SDQ-DP) in middle childhood (9-13 years of age) and includes the potential impact of clinical and psychosocial characteristics. METHOD: The data set was available from the BELLA study on mental health and well-being in children and adolescents, which is the mental health module of the German Health Interview and Examination Survey for Children and Adolescents (KiGGS). A representative epidemiological sample of 564 children living in Germany was examined at three assessment points over 2 years (data collection 2003-2006). The SDQ-DP of children aged 9-13 years was evaluated using Latent Class Growth Analysis (LCGA). RESULTS: For both genders three trajectories with low (girls 67.0% and boys 59.5%), moderate (girls 28.0% and boys 31.7%) and high SDQ-DP (girls 5.0% and boys 8.8%) scores were detected. The courses of low and moderate subgroups were stable, while in the high SDQ-DP subgroup boys showed a decreasing and girls an increasing trend in symptom severity on a descriptive level. The results of the multinomial logistic regression analyses revealed a significant influence of mainly externalising but also internalising problems both increasing the risk of moderate and high SDQ-DP in both genders. Good quality of life was a protective factor for the SDQ-DP course in all subgroups. CONCLUSION: In addition to the known clinical and scientific value of the SDQ-DP, three distinguishable trajectories of SDQ-DP in boys and girls could be found. High externalising problems at the beginning of the trajectory were associated with an undesirable course of SDQ-DP. These findings might be helpful for better psychoeducation, counselling and monitoring in clinical cases and public health.