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Abstract Background Early childhood development (ECD) is essential in human capacity building and a critical element in the intergenerational process of human development. In some countries, social programs targeted at improving ECD have proven to be successful. Oaxaca is one of the States with the greatest social inequities in Mexico. Therefore, children in Oaxaca are at a high risk of suboptimal ECD. In 2014, the non-governmental organization (NGO) Un Kilo de Ayuda started to implement the Neurological and Psycho-affective Early Childhood Development Program in eighty marginalized communities of Oaxaca. In this article, we present the impact evaluation design to estimate the effect of this program on ECD. Methods We will use a cluster randomized stepped-wedge design with an allocation ratio of 1:1. Communities will be randomly assigned to each study group: four groups of twenty communities each. We expect that children from intervened communities will show better ECD outcomes. Discussion This study is one of the few rigorous assessments of the effect of an ECD program on the neurodevelopment of Mexican children recruited in their first 3 years of life from communities of high social vulnerability. Our study design is recommended when the way in which outcomes are measured and assessed depends on age, self-selection is present, and assignment is performed at an aggregate level. Implementation research will be conducted prior to study launch and quality control measures will be in place to maximize the fidelity of study design implementation. Trial registration ClinicalTrials.gov NCT04210362

Early childhood development (ECD) is a critical stage in the intergenerational process of human development. Targeted interventions depend on accurate and up-to-date ECD measurements. This paper presents estimates for the nutritional and neurodevelopmental status of socially marginalized children in Mexico. We performed a cross-sectional study based on data collected in 2019–2020 during home visits to 1,176 children aged 0–38 months across 24 highly marginalized locations in Oaxaca. We assessed nutritional status according to the World Health Organization 2006 child-growth standards and ECD status using the Child Development Evaluation Test, 2nd Edition. We stratified results by sex. Prevalence of stunting was 5.3 percentage points (p.p.) higher (p = 0.023) in males (25.3%; 95% CI: 20.2%, 31.1%) compared to females (20.0%; 95% CI: 15.0%, 26.1%). Overall prevalence rates stood at 5.7% (95% CI: 4.0%, 8.1%) for underweight, 1.5% (95% CI: 0.9%, 2.7%) for wasting and 3.6% (95% CI: 2.3%, 5.7%) for overweight/obesity, with no significant differences by sex. Prevalence of normal development was 8.3 p.p. lower (p = 0.001) in males (39.3%; 95% CI: 34.5%, 44.4%) compared to females (47.6%; 95% CI: 41.6%, 53.6%). By development area, the highest prevalence of suboptimal outcomes among children with developmental lag or at risk of delay was observed in their gross motor and language skills: 24.1% (95% CI: 20.0%, 28.8%) and 38.6% (95% CI: 34.0%, 43.3%), respectively. The largest difference between the sexes was found in the language area. Our results show that childhood development strategies have been insufficient thus far in the studied population. Programs specifically designed to prevent ECD lags and bridge inequality gaps are urgently needed. Trial registration: ClinicalTrials.gov ID: NCT04210362.