Weight-for-height Z-score (WHZ) and mid-upper arm circumference (MUAC) are two independent anthropometric indicators for diagnosing and admitting children with severe acute malnutrition (SAM) for treatment. While severely wasted children are at high risk of mortality, MUAC and WHZ do not always identify the same population of children as having SAM. Understanding how this discrepancy relates to age and sex may provide valuable information for care programmes for children with SAM. Age and sex distribution for differences between children identified as SAM by MUAC and WHZ were examined and the degree of agreement calculated. Children (n = 4297) aged 6-59 months with validated anthropometric measures were recruited from a population-based survey conducted in rural southern Ethiopia. MUAC < 115 mm and WHZ < -3 were used to define severe wasting as per the World Health Organization (WHO) classification. The kappa coefficient (κ) was calculated. There was fair agreement between the MUAC and WHZ definitions of severe wasting in boys (κ = 0.37) and children younger than 24 months (κ = 0.32) but poor agreement in girls (κ = 0.15) and children aged 24 months and above (κ = 0.13). More research is needed on response to treatment and prediction of mortality using different anthropometric measurements in relation to ages and sex of children.