Objective: The Ages and Stages Questionnaires Edition 3 (ASQ-3) are a well-validated international screen for developmental delays in young children. However, previous studies demonstrate variable scores between children eligible to take the same ASQ-3 interval. This study aimed to determine a relationship between age and ASQ-3 score for each screening interval. Methods: This was a baseline exploratory cross-sectional study of infants under 2 years old evaluated for the Peruvian social programme Cuna Más. Participants were included in Cuna Más if they lived in districts with fewer than 2000 inhabitants or 400 homes, indicating a predominantly rural population. The appropriate ASQ-3 screening interval was administered to each subject. Subjects were divided into four 2-week chronological subgroups based on age within each 2-month screening window and aggregated across all 12 screening intervals. Fisher's exact test, analysis of variance and Bonferonni post hoc test were used to compare differences between age subgroups. Linear regression was performed to assess the relationship between ASQ-3 score and both aggregated and disaggregated age subgroup. Results: A total of 5850 Peruvian infants were evaluated in 2013. Mean age was 13 ± 6.6 months, 50.7% were male and mean maternal education was 6.6 ± 4.0 years; 34.8% infants were stunted, 7.8% were underweight, 0.9% were wasted and 2% had age adjusted greater than 35 days for prematurity for ASQ-3 interval assignment. Mean total ASQ-3 was 42.2 ± 8.2. The ASQ-3 allocated 49.6% with suspected delay in one or more developmental areas. Before and after adjusting for wealth quintile, maternal education level, infant nutritional status and prematurity adjustment, age subgroup remained significantly associated with total ASQ-3 score (β = 1.8, CI: 1.7–2.0, P < 0.001), sectional ASQ-3 score (all P < 0.001) and inversely associated with one or more scores indicating suspected developmental delay (P < 0.001). Conclusions: The ASQ-3 may underestimate the sensitivity of child development to small differences in age in this population.