A previous whole-genome association analysis identifiedlysine demethylase 6A(KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity.KDM6Agene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goatKDM6AmRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect onKDM6Agene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats.KDM6AmRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying thatKDM6Amay have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P< 0.01), and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P< 0.05). There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P= 0.001). Consistently, the 16 bp indel also had a significant effect onKDM6Agene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel inKDM6Amay be useful for marker-assisted selection (MAS) of goats.