Southeast Asia's transition to rice agriculture is often used as an exception to the general pattern of health decline at the agricultural transition. Niah Cave is the largest known Southeast Asian Neolithic cemetery, providing valuable information about subadult health during the agricultural transition in this region. This study examines the health status and mortuary treatment of subadult skeletal remains (Minimum Number of Individuals (MNI) = 49) from the Neolithic cemetery of Niah Cave, Sarawak, Malaysia (1500–200 bc). This study found that few cases of cribra orbitalia (4.6%) and porotic hyperostosis (14%). However, nonspecific infections may have been a risk factor for subadults as over half (65%) died with active cases of periosteal reactions on their long bones. Differential diagnosis determined that possible factors for this include parasite load, rickets and scurvy. Mortuary practices indicate that subadults may have been treated differently in phases 1 and 2 but were grated similar mortuary treatment in phases 3 and 4. This study suggests that changes in mobility patterns may have placed subadults at risk for increased parasite load and vitamin deficiency, while the role of subadults within the community may have changed over time. Copyright © 2017 John Wiley & Sons, Ltd.