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Lethal recessive alleles that act prenatally may be detected from the absence of homozygous individuals in a population. However, these alleles may be maintained at relatively low frequencies in populations as heterozygotes. In pigs, they may reduce litter size. This study aimed to detect putative lethal variants in the Duroc breed. Phenotypes for the numbers of piglets born (TNB), born live (BA), alive at 24 h (L24), stillborn (SB), and born as mummified fetuses (MM) were available from 5340 recorded litters which resulted from mating of 192 genotyped boars with sows of unknown genotype (dataset 1). An additional 50 litters were produced from parents that were both genotyped (dataset 2). Imputed genotypes of 650K SNPs for 1359 Duroc boars were used in this study. One significant SNP (Bonferroni corrected P = 5.5E-06) was located on SSC14 with 45.3 homozygous individuals expected but none observed. This SNP was significant for mummified fetuses. One hundred fifty two haplotypes were also found to potentially harbor recessive lethal mutations. Twenty-one haplotypes had a significant harmful effect on at least one trait. Two regions, located on SSC8 (144.9–145.5 Mb) and SSC9 (19–19.4 Mb) had significant effects on fertility traits in both datasets. Additionally, regions on SSC1 (82.0–82.8 Mb), SSC3 (73.3–73.7 and 87.1–87.5 Mb) and SSC12 (35.8–36.2 and 50.0–50.5 Mb) had significant deleterious effects on TNB or BA or L24 in dataset 1. Finally, a region on SSC17 (28.7–29.3 Mb) had significant effects on TNB, BA and L24 in dataset 2. A few candidate genes identified within these regions were described as being involved in spermatogenesis and male fertility (TEX14, SEP4, and HSF5), or displayed recessive lethality (CYP26B1, SCD5, and PCF11) in other species. The putative loci detected in this study provide valuable information to potentially increase Duroc litter size by avoiding carrier-by-carrier matings in breeding programs. Further study of the identified candidate genes responsible for such lethal effects may lead to new insights into functions regulating pig fertility.