The aim of the study was to identify the factors associated with undernutrition indicators in children 5 years and younger in a rural community in Malaysia. A total of 295 children and their carers were selected from community clinics based on a multistage sampling method. Pretested questionnaire, anthropometric measurement, and dietary assessment were used for data collection. There was 69% stunting, 63.4% underweight, 40% wasting, and 26.8% with mid-upper-arm circumference (MUAC) for age below a z score of -2 among children. In all, 10 factors were found to be associated with different indicators of undernutrition. Age was the only factor that had association with all the undernutrition indicators. Total household income and total expenditure showed significant association with underweight. Birth weight was reported to have significant association with underweight, stunting, and low MUAC-for-age. The findings suggest that the factors of undernutrition were different for different indicators of undernutrition and thus give a more comprehensive picture on factors contributing to acute and chronic malnutrition.