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Background: The World Health Organization recommends weight-for-height Z-score (WHZ) or mid-upper arm circumference (MUAC) and bilateral pitting edema to diagnose acute malnutrition among children aged 6–59 months. WHZ and MUAC identify different sets of children with acute malnutrition, and overlap between their prevalence varies greatly among countries. Objective: The objective of the study was to determine the degree of overlap and agreement between WHZ and MUAC to diagnose children with acute malnutrition in India. Methods: Five nutrition surveys using Standardized Monitoring and Assessment of Relief and Transitions methodology were conducted in four Indian states. A total of 2127 children aged 6–59 months were analyzed. All anthropometric indices were calculated using emergency nutrition assessment software and analyzed in Epi-Info 3.5.4. Results: Of total global acute malnutrition (GAM) cases, 96% and 28.4% cases were diagnosed with WHZ and MUAC, respectively. Similarly, of total severe acute malnutrition (SAM) cases, 95.1% were identified using WHZ and 30% using MUAC. The proportion of overlap between the two criteria for GAM and SAM cases was 24.5% and 25.2%, respectively. The analysis showed that MUAC was comparatively more sensitive to identify acute malnutrition among 6–23-month aged children and females. Conclusion: One-fourth of GAM and SAM cases were identified with both criteria. MUAC identified approximately 30% of the total SAM cases which was lower than other countries. MUAC identified more number of females and younger children, who may have higher mortality risk and would result significantly smaller caseload (68% smaller) that requires intervention compared to when using WHZ.