Abstract Background Left behind children (LBC) are children living with caregivers, while their parents work abroad. In recent decades Lithuania had lost ¼ of its population due to emigration, but the prevalence of LBC and their health needs are not sufficiently studied. The aim of study was to evaluate the association between self-reported health, emotional and behavioural difficulties between LBC and non-LBC. Methods The cross-sectional study was approved by the Biomedical Research Ethics Committee, No. 2021/11-1378-861. In March 2022, this pilot study collected data from adolescents aged 12-17 years at three randomly selected schools from the migration affected regions. Parents and children provided informed consent to participate in pilot study. Self-reported measures collected from the participants: Strengths, and Difficulties Questionnaire (Goodman, 2005) and a questionnaire on demographics and on the health situation. Chi2 tests and logistic regression were calculated by using Stata (version 15.1). Results The sample consisted of 127 children (mean age 15.2, SD 1.27; 54 boys, 72 girls) including 39 LBC. Mostly fathers left to work abroad (n = 36), but majority of children (n = 36) regularly communicated remotely with their migrated parents. Binary logistic regression results show that LBC children tend to evaluate their health as ‘poor, ‘bad', or ‘very bad’ (OR 2,33; 95CI [1,02-5,33]). There were no differences for emotional and behavioural problems. Preliminary results from multiple regression model showed that children with self-reported emotional/behavioural difficulties (OR 3,06; 95CI [1,12-7,84]), females (OR 4,99;95CI [1,55-16,13]) and LBC (OR 2,44; 95CI 0,95-6,25]) more likely evaluate their health as ‘poor', ‘bad’ or ‘very bad’ (likelihood-ratio test=23,72; model p < 0.001). Conclusions This pilot study found negative association between parental migration and children’s self-reported health. However, a more comprehensive study with a larger sample size is needed. Key messages • Pilot study suggests negative association between parents migration and children’s self-reported health. • More comprehensive study in bigger sample for the emotional/behavioural/communication difficulties between left behind children needs to be done.