<i>Background and Methods:</i> We conducted a large-scale case-control study that explored the association of 358 single nucleotide polymorphisms (SNPs) in 185 patients with end-stage renal disease. A variety of SNPs were recognized as significant in simple association studies. In addition, haplotype analysis identified the gene for the alpha 1C subunit of the voltage-dependent L-type calcium channel (CACNA1C) as having a significant association with secondary hyperparathyroidism (intact parathyroid hormone level >200 pg/ml) among 61 haplotypes. Since CACNA1C is a relatively large molecule, we examined 84 SNP markers from the CACNA1C region located on chromosome 12 by haplotype case-control association analysis. <i>Results:</i> Sixteen SNPs of 14 genes were significant according to allelic and/or genotypic studies (p < 0.05 by Fisher’s exact test). Three different SNPs were from the CACNA1C gene. Next, we performed haplotype-based association testing with a focus on the CACNA1C region, revealing an odds ratio (OR) of 1.63 and 95% confidence interval (CI) of 1.05–2.52. The second major haplotype with a frequency of 27% was also significant and acted as a protective haplotype (p = 0.022 by Fisher’s exact test, with an OR of 0.55 and 95% CI of 0.33–0.90). <i>Conclusion:</i> These results suggest that CACNA1C may be associated with secondary hyperparathyroidism. In addition, the haplotype-based approach may be useful to screen for key molecules associated with complex traits.