To analyse the association of socio-demographic and health factors with vitamin D insufficiency and 25-hydroxyvitamin D (25(OH)D) concentration in Brazilian children aged 6–59 months. Data from 8145 children from the Brazilian National Survey on Child Nutrition (ENANI-2019) were analysed. The serum concentration of 25(OHD)D was measured using a chemiluminescent immunoassay. The prevalence of vitamin D insufficiency (25(OH)D < 50 nmol/l) and 95 % CI was calculated. Logistic and linear regression models were used to identify the variables associated with vitamin D insufficiency and serum 25(OH)D concentrations, respectively. The mean 25(OH)D concentration was 98·6 ± 36·0 nmol/l, and 4·3 % of the children presented vitamin D insufficiency. Children aged 6–23 months (OR = 2·23; 95 % CI 1·52, 3·26); belonging to Southeast (OR = 5·55; 95 % CI 2·34, 13·17) and South (OR = 4·57; 95 % CI 1·77, 11·84) regions; the second tertile of the National Wealth Score (OR = 2·14; 95 % CI 1·16, 3·91) and winter (OR = 5·82; 95 % CI 2·67, 12·71) and spring (OR = 4·84; 95 % CI 2·17, 10·80) seasons of blood collection were associated with a higher chance of vitamin D insufficiency. Female sex (β = −5·66, 95 % CI − 7·81, −3·51), urban location (β = −14·19, 95 % CI −21·0, −7·22) and no vitamin D supplement use (β = −6·01, 95 % CI −9·64, −2·39) were inversely associated with serum 25(OH)D concentration. The age of children and the Brazilian geographical region of household location were the main predictors of vitamin D insufficiency. In Brazil, vitamin D insufficiency among children aged 6–59 months is low and is not a relevant public health problem.