Lipoprotein(a) [Lp(a)] is a LDL-like particle containing a single copy of apolipoprotein B-100 (apoB-100), covalently attached to apolipoprotein(a) [apo(a)]. Apo(a) is encoded by LPA gene (6q26-27), and it has been hypothesized that LPA +93C>T and +121G>A polymorphisms in the 5' flanking region could influence the apolipoprotein(a) synthesis, so affecting Lp(a) levels. In order to permit a rapid detection of LPA polymorphisms, we performed an analysis protocol for the SNPs detection through Nanogen Technology with the Universal Reporting System, and we compared our results with those obtained with a more conventional method, such as PCR-RFLP assay. Our experiments evidenced that Nanogen Technology may be used as a high-throughput tool in LPA +93C>T and +121G>A polymorphisms analysis, minimizing the hands-on time and the costs for the SNPs detection. In particular, this Technology allows the analysis of polymorphisms at the LPA locus, able to modulate the levels of Lp(a), a relevant marker of atherosclerosis.