A cross-sectional anthropometrics survey was carried out in a low-income community of Surabaya, Indonesia, to examine the association between mother's employment and the child's nutritional status for identifying a group at risk of having malnourished children. Subjects were 274 children under the age of 5. The children of non-working mothers had significantly higher height-for-age z-score (HAZ) (p < 0.05) than those of working mothers. When mother's work was divided into 'formal' and 'informal', HAZ and weight-for-age z-score (WAZ) of children of the informal worker's group were significantly lower than those of the non-working mother and the formal worker's group (p < 0.05). Mother's education and income of the formal worker's group were significantly higher than those of the informal worker's group (p < 0.01). Our study identified a group at risk of malnutrition, i.e., children of mothers working in informal sectors. The programs to provide childcare for working mothers should target this particular group of poor households.