Synaptosomal-associated protein 25 (SNAP-25) plays a crucial role in exocitosis. Single nucleotide polymorphisms (rs3746544 and rs1051312) in the 3' un-translated region of the SNAP-25 gene have been described to be in association with attention-deficit hyperactivity disorder. As the disease affects millions of children world-wide, understanding the genetic background of attention-deficit hyperactivity disorder is of crucial importance. Efficient and reliable PCR-RFLP protocols were elaborated for the genotyping of the rs3746544 and rs1051312 SNPs employing a high-throughput capillary electrophoresis method for fragment analysis. A novel real-time PCR-based technique was used applying sequence specific TaqMan probes to haplotype the two SNPs, and the G-C haplotype could not be detected in a large Caucasian population (N = 1376). These findings have been confirmed by molecular biology tools as well as by the PHASE Bayesian computational approach. In silico analyses have suggested that the two SNPs might alter microRNA binding and thus have an effect on SNAP-25 production. We have demonstrated that this biological information can be revealed only by direct haplotype analysis emphasizing the importance of our novel molecular haplotye analysis protocol. Results of the study of the two SNPs might shed light on the association of SNAP-25 variants and pathological phenotypes at the molecular level.