Background
Pakistan ranks third lowest on a global gender index (2013) and 13th highest on the prevalence of underweight among under-five children (2010). Through this population-based study, we examined gender differentials in the prevalence of stunting, wasting and under-weight defined by World Health Organization (WHO) Growth Standard among rural pre-school Pakistani children.

Methods
We performed secondary analysis of data collected through a cross-sectional survey of Thatta district during 1992-93. Prevalence ratios were calculated for 1051 children aged 0-35 months from 95 randomly selected villages of rural Pakistan using a clustered adjusted log binomial model. Level 1 variables included child and household characteristics and level 2 included village characteristics.

Results
Based on the new WHO growth reference, a major proportion of children were stunted (52.9 %), wasted (22.9 %) and under-weight (46.5 %). In a two-level model, compared to boys, girls had significantly greater risk of stunting [Prevalence Ratio (PR) (95 % C.I.)?=?1.18 (1.03, 1.36)] and under-weight [P.R. (95 % C.I.) 1.14 (1.03, 1.26)], after adjustment of maternal literacy and village variables. Risk of wasting did not differ with gender [P.R. (95 % C.I.)?=?1.04 (0.99, 1.15)]. Mothers of stunted and underweight children were respectively, 21 and 20 % more likely to be illiterate than those of normally nourished children. Sick children were at 16 % greater risk of wasting than those not reported ill.

Conclusion
Greater prevalence of stunting and under-weight among girls suggests adoption of a gender sensitive approach in nutritional intervention programmes. Prompt management of childhood illnesses may reduce prevalence of wasting. Better literacy among rural mothers may reduce prevalence of stunting and under-weight. Whether gender differences in nutrition status are an underlying pathway for excessive girl mortality in rural Thatta needs further examination.