Fertilization and development of the preimplantation embryo is under genetic control. The present goal was to test 434 single nucleotide polymorphisms (SNPs) for association with genetic variation in fertilization and early embryonic development. The approach was to produce embryos from 93 bulls using in vitro procedures (n = 3–6 replicates per bull) and relate cleavage rate (CR) and development of cleaved embryos to the blastocyst stage (BDRC) to the genotype for each SNP. Bulls were selected to have either high or low estimates for predicted transmitted ability for daughter pregnancy rate (DPR), an estimate of female fertility. The repeatability was 0.84 for CR and 0.55 for BDRC. Semen extender affected CR, with lower results for milk extender than yolk extender. There was no significant correlation between DPR and either CR or BDRC. A total of 100 SNPs had a minor allele frequency sufficiently high (>5%) to allow association analysis. There were nine genes with SNPs associated with CR (AVP, DEPP, EPAS1, HSD17B6, NT5E, SERPINE2, SLC18A2, TBC1D24, and a noncharacterized gene) and 12 genes with SNPs associated with BDRC (C1QB, FAM5C, HSPA1A, IRF9, MON1B, PARM1, PCCB, PMM2, SLC18A2, TBC1D24, TTLL3, and WBP1). Results demonstrate that in vitro fertilization and blastocyst development are under genetic control and point out the potential importance of some previously unknown genes in these processes. Selection of cattle based on the genotype at one or more of these 19 loci may prove useful in conjunction with other genetic markers for improving genetic ability for fertility.