<p class="abstract"><strong>Background:</strong> Nepalese society is traditionally patriarchal and son-preferred with increasing numbers of sex-selective abortions. In this context, this study aims to assess the gender preference and associated factors among pregnant women visiting the antenatal care ward of a large public maternity hospital in Kathmandu, Nepal.</p><p class="abstract"><strong>Methods:</strong> A hospital-based cross-sectional study was carried out among 821 antenatal women. Data was collected via face to face interview with structured questionnaire, and gender preference was assessed using Coombs’ scale.  </p><p class="abstract"><strong>Results:</strong> At the first instance, more than half 56.2% respondents wished to have two sons and one daughter if they were to have only three children. On asking further questions as per the Coombs’ scale, about 40% of the respondents had son preference falling in IS scale 7-5, 33% had balanced IS-4, and 27% had daughter preference (IS 3-1). The respondent characteristics significantly associated with gender preference were ecological region (p=0.007), education (p=0.009), marital duration (p=0.044) and parity 0.32.</p><p class="abstract"><strong>Conclusions:</strong> The wish to have son is prevalent among the respondents followed by a mixed gender of children. Educational status, ecological region, and parity explain this differential wish. Women’s education and autonomy are the areas to tackle with sex bias of offspring.</p>