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Vitamin A deficiency is a global health problem and can be effectively alleviated through crop biofortification. Quantification of carotenoids using high-performance liquid chromatography is expensive and time-consuming, thereby posing a challenge in the selection of genotypes with high provitamin A. Favourable alleles possessing rare genetic variation in lycopene-ε-cyclase (lcyE) and β-carotene hydroxylase (crtRB1) genes are associated with higher accumulation of provitamin A, especially β-carotene; and selection of these alleles holds immense promise in reducing large-scale phenotypic assays. Screening of a diverse set of 385 maize inbred lines of indigenous and exotic origin detected the presence of two alleles (amplicon size: 250 and 650 bp) of lcyE and three alleles (amplicon size: 296, 543 and 875 bp) of crtRB1 in the inbred panel. Favourable alleles of both the genes were rare among the traditional maize germplasm; 3.38% of the inbreds possessed the favourable allele (650 bp) of lcyE, while 3.90% inbreds had the favourable allele (543 bp) of crtRB1. Five inbreds (1.3%) with favourable alleles of both the genes were found. Inbreds with favourable alleles of crtRB1 and lcyE serve as rich genetic resources for effective utilization in the maize biofortification programme.