Single-nucleotide polymorphisms (SNPs) within the genes of factor V (FV) (G1691A; exon 10), prothrombin (FII) (G20210A; 3'untranslated - region) and methylenetetrahydrofolate reductase (MTHFR) (C677T; exon 4) are associated with hypercoagulability, and systematic screening of individuals being at higher risk of thrombosis has been suggested. SNPs in the 2q33 region within the genes of CD28 (+17T/C; intron 3) and CTLA4 (-318C/T; promoter and +49A/G; exon 1) are likely to affect T-cell proliferation and antigen presentation signaling, which may lead to altered sensitivity of allograft or self-tissue recognition and affect the incidence of autoimmune diseases. We developed primers that allow specific amplification of these six SNPs at test conditions identical with those used for HLA typing with the CTS PCR-SSP reagents. One hundred ninety-six healthy German Caucasian individuals were tested for the six SNPs. The genotype frequencies for all SNPs were in Hardy-Weinberg equilibrium. There was no significant difference in the distribution of genotypes when compared to other published studies in which these SNPs were tested. The described PCR-SSP method can be used to screen large numbers of patients for these SNPs.