Background: Stunting impairs child growth and development, affecting millions of children under five years worldwide. Consumption of milk provides important macronutrients and micronutrients that support growth. Objectives: To assess milk consumption and its associations with stunting in children aged 6-59 months in Surabaya City, Indonesia. Method: This case-control study compared milk consumption between children aged 6-59 months with stunting (cases) and normal children (controls). Data were obtained from questionnaires and anthropometric databases from five primary healthcare centres in Surabaya city. Data from 94 subjects were analysed using Chi-square and multivariate logistic regression. Results: Children with stunting had a significantly later age of milk introduction, less frequent daily milk consumption and a lower amount of daily milk consumption than controls (p<0.05). Age of milk introduction ≥18 months was a risk factor associated with stunting (p<0.05, crude OR= 3.0, 95% CI 1.2-7.4). Daily milk consumption less than twice a day (p<0.05, crude OR=3.8; 95% CI 1.4-10.5) and amount of milk less than 500 ml (p<0.05, crude OR=2.9; 95% CI 1.2-6.8) were risk factors associated with stunting. After adjusting for other confounding variables, odds of stunting were found to be dominantly higher statistically in children with daily milk consumption of less than twice a day (p<0.05, adjusted OR= 3.4, 95% CI 1.0-11.5). Conclusions: This study concluded that milk introduction at the age beyond 18 months, frequency of daily consumption of less than twice a day and an amount of less than 500 ml a day are significantly associated with higher odds of stunting.