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Objective Children from agricultural families are often para-occupationally exposed to pesticides. We associated urinary biomarkers of pesticide exposure with relative telomere length (rTL) and mtDNA copy number (mtDNA-cn) in 270 5-year-old children from agricultural families who participated in the Infants’ Environmental (ISA) birth cohort.Methods We repeatedly measured biomarkers of pesticide exposure in maternal urine during pregnancy and in children’s urine at 5-years. rTL and mtDNA-cn were determined in children’s saliva, relative to a single-copy hemoglobin beta gene, using real-time PCR. We associated log10 transformed mean urinary biomarker concentrations with log10 transformed rTL and mtDNA-cn, using separate multivariate linear regression and generalized additive models, and adjusted for possible confounders.Results Exposure to fungicides and 2,4-D was associated with changes in rTL and mtDNA-cn. Higher prenatal hydroxy-thiabendazole was associated with shorter rTL, while current 2,4-D was associated with longer rTL:%-change-in-β (95%CI) = -0.19 (-0.36, -0.02) and = 0.38 (0.01, 0.75) per tenfold increase in exposure, respectively. In addition, prenatal hydroxy-pyrimethanil was slightly associated with mtDNA-cn: β =0.33 (-0.05, 0.70) and 2,4-D was non-linearly associated with mtDNA-cn (estimated degrees of freedom of smoothed beta = 2.78, p=0.04), while current urinary ethylene thiourea (biomarker of mancozeb) and hydroxy-tebuconazole were associated with decreased and increased mtDNA-cn:%-change-in-β (95%CI) = -0.84 (1.71, 0.05) and 0.71 (0.01, 1.40), respectively. Biomarkers of pyrethroid and chlorpyrifos exposure were not associated with rTL or mtDNA-cn.Conclusions Prenatal and childhood exposure to fungicides and 2,4-D may alter rTL and mtDNA-cn, which is of concern as shorter TL may reflect an increased risk of age-related diseases. Longer TL might reflect changes in cellular aging, including increased cellular mutation risks. Finally, increased mtDNA-cn indicates compensation for oxidative stress, while decreased levels reflect oxidative stress.