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There is limited literature from India on effect of fathers' deployment on the mental health of children. This cross-sectional analytical study investigates the difference in anxiety levels of children whose fathers are deployed in a field location and compares it with children currently located with their fathers. Data were collected in an army school from 200 children aged 10–17 years with fathers deployed in field locations (n = 99) and fathers currently residing with the children (n = 105) via interviewer administered and self-completed Screen for Child Anxiety-Related Disorders (SCARED) questionnaire. Anxiety scores were on an average, minimally raised above the cut-off level for children who had fathers deployed. In addition, panic disorder scores were also above the cut-off levels for these children. While scores were normal in all other domain, they were higher than that for children residing with their fathers, although the difference was not significant. Girls with fathers deployed had scores higher than cut-off scores for domains such as panic, separation anxiety and school avoidance, while boys had scores higher than cut-off scores only for panic disorders. However, the girls had significantly higher scores than boys in all domains. Girls in both groups (with and without father deployed) had higher scores than cut-off scores for panic disorders. Anxiety levels in children were not found to be unduly affected by the deployment of fathers. But girls were found to have clinically relevant panic disorder, school avoidance and separation anxiety scores as compared with boys in the similar situation of parental separation. [ABSTRACT FROM AUTHOR]