None of the SNPs showed a significant association with MDD, but a SNP (rs2075984) in CSNK1E and SNP (rs6502097) in CSNK1D were associated with SCZ (P = 0.0091, uncorrected) and BD (P = 0.030, uncorrected), respectively. To confirm these findings, we analyzed an independent dataset (maximum N = 3815) but found a lack of association (P = 0.63 for rs2075984 and P = 0.61 for rs6502097). The final meta-analysis showed no association between these SNPs with SCZ (P = 0.21) and BD (P = 0.53). These results do not support that genetic variation in CSNK1D and CSNK1E is a susceptibility factor for major psychiatric disorders in the Japanese population.