Background: The limestone caves and rock shelters of the Nenggiri Valley in the state of Kelantan are sites of archaeological excavation since early 20th century. Recently, in November 2018, an almost complete female skeleton was uncovered in Gua Chawan, one of the caves in the Nenggiri Valley. Her age was estimated to be in the mid-thirties based on dental examination. The skeleton was carbon-dated by Beta Analytics, USA to be around 8000 years old, i.e. corresponding to the early Mesolithic period. No study on the structural properties of prehistoric Malaysian skeletal remains have ever been done. Objective: Our objective was to determine the mineral content, density, and microarchitecture of this prehistoric skeleton and compare it with modern human skeletons. Methodology: The right humerus from the prehistoric skeleton was compared with 6 modern humeri obtained from the Anatomy Department. The humeri were weighed and measured. Bone mineral content and density were measured using Dual-Energy X-Ray Absorptiometer (DXA). Bone microstructure was determined using micro Computed Tomography (microCT). Results: Amongst the 7 humeri studied, the prehistoric humerus was the second longest, but second lightest in weight. The bone mineral density (BMD) was the second highest. MicroCT scan was done on the prehistoric humerus and two other humeri with almost similar BMD. MicroCT data showed that the prehistoric humerus had higher bone volume and trabecular number, while the trabecular separation was the smallest. Conclusion: The prehistoric skeleton was more dense than the modern bones, maybe due to the higher levels of physical activity and healthier, more organic nutritional intake of that time period. Limitations: Only one prehistoric skeleton was available for study, while the age and gender of the modern humeri were not known. Other factors related to the environment in the cave and length of time the skeleton was there were not considered.