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Background Son preference is predominant in developing countries especially South Asian countries and its effect is most visible when the fertility is on transition. Nepal is a country in South Asia where the fertility has declined and son is valued highly. This study examines the parent’s gender preference for children and its effect on fertility and reproductive behaviors. Methods Study was conducted in Sonapur village development committee of Sunsari district among women of Tharu community of reproductive age (15–49) currently in union and having at least one child. Data was collected by house to house survey. Data was analyzed with IBM SPSS 20 version. Multinomial and binary logistic regression were used to analyze the relationship among variables. Results Three hundred women of reproductive age were included in the study. Current average age of the respondents was 31.97 years and mean age at marriage was 18.87 (SD +/-2.615). Child Sex ratio (male: female) of the respondents who didn’t want any more children was 1.41. The birth spacing following male baby was 3.09 years whereas the average birth spacing following female baby was 2.71 years. Age of the respondents and education status of the respondents were also significantly associated with contraceptive practice. Presence of only female children in family significantly increased the desire of other children (AOR = 10.153, 95% CI = 2.357-43.732). Conclusion This study finds that the gender preference affects the fertility and reproductive behavior of the respondents and it is necessary to reduce son preference for the health and well being of children and women.