Background Evidence suggests free mono-hydroxyvitamin D (25[OH]D) concentrations are more strongly linked to certain outcomes than total concentrations; however, no studies have examined the relation between free 25(OH)D and respiratory or allergic disease. Objective To examine associations between total and free 25(OH)D concentrations and asthma outcomes. Methods We quantified total and free 25(OH)D concentrations in 137 Peruvian children with asthma and 152 children without asthma and examined associations with asthma outcomes. Results Mean age ± SD was 13 ± 2.5 years, and 50.2% were boys. Mean total and measured free 25(OH)D concentrations were 29 ± 9.5 ng/mL and 5.0 ± 1.3 pg/mL, respectively. Lower free but not total 25(OH)D concentrations were significantly associated with atopy in all children (total, odds ratio [OR] 1.3 per 10-ng/mL decrease, 95% confidence interval [CI] 0.95–1.7, P =.12; vs free, OR 1.3 per 1-pg/mL decrease, 95% CI 1.0–1.6, P =.02) and children with asthma (total, OR 1.1 per 10-ng/mL decrease, 95% CI 0.75–1.7, P =.57; vs free, OR 1.6 per 1-pg/mL decrease, 95% CI 1.0–2.5, P =.04). Free but not total 25(OH)D levels were significantly associated with pre-bronchodilator forced expiratory volume in 1 second (total, 0.11 L, −0.12 to 0.34, P =.34; vs free, 0.20 L, 0.021–0.39, P =.03) and forced vital capacity (total, 0.13 L, −0.12 to 0.37, P =.31; vs free, 0.22 L, 0.026–0.42, P =.03) Z-scores in children with asthma. Conclusion Atopy, forced expiratory volume in 1 second, and forced vital capacity were more strongly linked to free than to total 25(OH)D concentrations, suggesting the free form might be more relevant in modulating allergic disease risk and pulmonary function in children with asthma.