Background: In Pakistan, preference for boys over girls is deeply culturally embedded. From birth, many women experience gendered disadvantages; less access to scarce resources, poorer health care, higher child mortality, limited education, less employment outside of the home and circumscribed autonomy. The prevalence of psychological morbidity is exceptionally high among women. We hypothesise that, among women of childbearing age, gender disadvantage is an independent risk factor for psychological morbidity. Methods. A cross-sectional catchment area survey of 525 women aged 18 to 35 years living in Islamabad and Rawalpindi. The effect of gender disadvantage was assessed as a latent variable using structural equation modelling. Indicators were parental gender preference, low parental care, parental overprotection, limited education, early age at marriage, marital dissatisfaction and low autonomy. Psychological morbidity was assessed using the 20 item Self Reporting Questionnaire (SRQ). Results: Gender disadvantage was independently predictive of psychological morbidity. Among married women, socio-economic status did not predict psychological morbidity, and the effect of education was mediated through gender disadvantage rather than socioeconomic status (SES). The women's own preference for a male child was strongly predicted by their perceptions of having been disadvantaged by their gender in their families of origin. Conclusions: The high prevalence of psychological morbidity among women in Pakistan is concerning given recently reported strong associations with low birth weight and infant stunting. Social action, public policies and legislation are indicated to reduce culturally embedded preferences. Neglect of these fundamentals will entrench consequent inequities including gender bias in access to education, a key millennium development goal.