Objective: To determine the correlation between dual energy X-ray absorptiometry (DEXA) and skin fold thickness (SKF) equations for estimation of body fat (BF) composition in secondary school children and validation of prediction equations by Slaughter, Goran and Dezenberg. Design: Cross sectional analytical study. Setting: Joint Commission for International Accredited ( JCIA) tertiary care hospital of Karachi, Pakistan from January 2010 to May 2010. Participants: The study was approved by the Hospital's ethical review committee. Written and verbal consents were obtained from principals of two schools and parents of 99 children (mean age of 14±1.89 years; min-max 9-19 years; 54 men and 45 women) accrued in study. DEXA scan was acquired and SKF was measured at angle of the scapula, iliac crest and mid-arm for bicep and tricep skin folds using Holtain Callipers. Correlations were established between estimated fat mass (FM) and per cent BF (%BF) calculated by DEXA and those predicted by prediction equations. On obtaining significant correlation of >0.5, overall accuracy, precision and bias was calculated. Results: There was an overall increased adiposity in females with FM of 3.57 kg and %BF 6.2% higher than male counterparts (p<0.05). Slaughter equation predicted %BF accurately with overall high accuracy, minimal bias and with good precision with DEXA. Dezenberg and Goran equations had significant bias in prediction of FM which was statistically significant with low level of accuracy of the Goran equation. Conclusions: We conclude that Slaughter equation for estimating %BF showed reasonable validation with DEXA. Nevertheless further studies with consideration for maturity and ethnicity are warranted for better results. However, for estimation of FM, previously formulated equations by Goran and Dezenberg showed significant difference in our population. We do recommend further studies for developing and validation of skin fold equations specific to Pakistani paediatric population.