Background: The microbiome and genetics, including variants in the 17q21 locus, have been separately linked to the development of childhood asthma, but the interplay between these factors in asthma risk is unknown. Objective: To understand how the intestinal microbiome and 17q21 variants interact in childhood asthma risk among offspring of participants in the Vitamin D Antenatal Asthma Reduction Trial (VDAART), a randomized controlled trial of prenatal vitamin D supplementation. Methods: 368 subjects with complete longitudinal stool microbiome and genotype data were included in this analysis. Microbial maturation at ages 3-6 months and 1 year was determined using a random forest model to predict age based on microbiome composition. We analyzed the functional 17q21 SNP, rs12936231, assuming a dominant model. We determined associations of microbial maturation and genotype risk with asthma or recurrent wheeze by age 3 years. Results: After adjusting for potential confounders, subjects with both intestinal microbial dysmaturity and a risk genotype had an increased odds of childhood asthma or recurrent wheeze compared to those with neither microbial dysmaturity nor risk genotype (microbial dysmaturity at 3-6 months: OR 18.8, 95% CI 3.33, 357.2, p=0.007; microbial dysmaturity at 1 year: OR 3.22, 95% 1.3, 9.2, p=0.02). There was a trend towards increased childhood asthma risk in subjects with either microbial dysmaturity or risk genotype compared to subjects with neither. Conclusions: We observed an additive effect of perturbed intestinal microbiome maturity and a 17q21 risk variant on childhood asthma or recurrent wheeze by age 3 years.