ApoCII is an important protein in lipid metabolism and transport as it is an activator of the lipoprotein lipase. The encoding gene spans 3.58kb consisting of 4 exons and 3 introns on chromosome 19q13.32. Several reports have documented many single nucleotide polymorphisms within the APOCII gene locus and very few have been shown to be associated with metabolic disorders. The aim of our study was to identify and analyze genetic variants by sequencing the full APOCII gene locus with its flanking sequences among a cohort of the Kuwaiti Arab population including a sample with dyslipidemia. Sequence analysis revealed 52 variants including 5 novel variants, among the samples tested and all were localized in the non-coding regions. There was no significant association of any of the variants (having a minor allele frequency above 0.05) with dyslipidemia. However, two variants were shown to be informative ethnic markers for the studied population. The study reports findings that add to the ongoing research which aims to identify genetic variants that are ethnic specific and play a role in lipid metabolism and transport. Further analysis in the genetic association of apolipoprotein genes and lipoprotein lipases can provide means to elucidate the molecular mechanisms of metabolic disorders.