Type 2 diabetes (T2DM) is a prime public health condition in Egypt. Along with the global development of T2DM, the frequency of T2DM diagnosed in adults < 40 years old has increased dramatically. Pancreatic B-cells express the MTNR1B gene, which expresses the receptor 1B of melatonin. Multiple large-scale genome-wide association studies and meta-analyses revealed a strong connection between the rs10830963 of the MTNR1B gene with fasting glucose and T2DM in many ethnic groups. This study aims to detect the link between rs10830963 and early-onset type 2 diabetes (EOD) in the Egyptian population. The rs10830963 was identified using polymerase chain reaction (PCR) followed by DNA sequencing technology on 12 T2DM patients and 18 healthy controls group with an age range of 30 to 39 years. Fasting blood sugar (FBS), glycated hemoglobin (HbA1c), serum creatinine (CREAT), triacylglycerol (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and very low-density lipoprotein cholesterol (VLDL-C) were determined for both healthy and diabetic groups.  Four T2DM patients (one male and three females) in addition to four healthy individuals (one male and three females) were found to contain the risk G allele when compared to the NCBI reference sequence using the T-Coffee online tool for multiple sequence alignment. Furthermore, the RNA secondary structure for reference and sample sequences with the rs10830963 was predicted in terms of minimum free energy (MFE) using the Vienna online tool, finding that there is a slight difference in MFE between the compared sequences, which may explain the upregulation of mRNA of the MTNR1B gene in presence of rs10830963. This study reveals a possible association between the MTNR1B gene variant rs10830963 and EOD in our Egyptian population sample.