Fresh honey is always seen as better than the use of old or stored honey for medicinal purposes. Long storage of honey can degrade certain compounds with increased HMF content, which can lower the quality of the honey itself. The present study investigates the variability of the content of two possible markers in Malaysian stingless bee (G. thoracica, H. itama and T. apicalis), namely glycerol (GCR) and myo-inositol (MYI) as a function of its storage time. In this work, GCR and MYI were detected and evaluated in all eight honey samples using the GC-MS method based on the NIST standard reference database. The average peak area abundance value for GCR at initial measurement was at 447,758,853+114,869,619 and decreased to 271,164,640+120,593,470 after 2 months of storage, whilst for MYI, initial measurement was 166,193,862+59,833,930 and reduced to 91,795,248+28,421,379 after 2 months of storage. Results showed that the samples kept at 4ºC decreased in the content of GCR and MYI about 24.56% and 28.84% respectively after two months of storage. The changes of GCR and MYI contents in honey can be used as possible marker compounds for honey freshness as a function of storage time.