Background: Body mass index (BMI) and triceps skinfold thickness thickness (SFT) are assessment tools for underweight, a major health problem in developing countries as well as emerging obesity and overweight. Objectives: To compare the use of BMI and SFT in determining the prevalence of underweight, overweight and obesity among primary school pupils in Abakaliki metropolis of Ebonyi State, South East Nigeria. Method: Eight hundred and four pupils (415 males, 389 females), aged 6-12 years, in four public and four private primary schools were selected by a multi stage random sampling. Four hundred and twenty-six (53.0%) subjects were in public schools while 378 (47%) were in private schools. Standard methods were used to determine the weight, height and triceps SFT of the participants. BMI values were calculated for each participant and compared with BMI for age and sex from World Health Organisation (WHO 2007) reference standard and SFT values compared with reference curves for triceps SFT in US children and adolescents for age and sex. The prevalence of underweight, overweight and obesity among our cohorts using BMI were 5.6% and 6.2%, 3% while using SFT, it was 29.2%, 1.6% and 0.9% respectively. Conclusion: The prevalence of underweight, overweight and obesity using BMI and SFT were not directly related. When subjected to Kappa analysis, it showed only fair agreement (K= 0.23) as values obtained using BMI were not similar to that obtained using SFT. BMI is more sensitive and specific, with minimal inter- and intra- observer errors. It is internationally more accepted standard, therefore preferred to SFT.