The migration makes an influence on children’s mental health and behaviors. However, the majority of studies investigate the families and people in migration rather than left-behind groups in their home countries. OBJECTIVE: to assess the possible impact of parents’ migration on emotional and behavioral problems of their left-behind children. The study comprised 10–19-year-old adolescents from five urban secondary schools (n = 1292). The cross-sectional study was conducted in Kaunas city (Lithuania). Main measures were self-reported scales – Strengths and Difficulties Questionnaire (SDQ) and Child Behavior Checklist (CBCL) as well as items on subjective perceptions and feelings towards the change of relationship with a missing parent due to migration or divorce. Findings show that left-behind children report more risky behaviors and emotional problems, they tend more to feel unloved (OR = 2.34, p < 0.05), longing for missing parent (OR = 4.72, p < 0.05), contemplating suicide or self-injuring behavior (OR = 3.92, p < 0.05). Emotional and behavioral problems are more prevalent among 15–19-year-old male adolescents (OR = 1.71, p < 0.05). The left-behind children report more emotional and behavioral problems compared to the children from divorced families. The findings suggest that parental migration has specific negative effects on left-behind children’s emotional state and behaviors.