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There is being analyzed polymorphism of maize genes associated with the formation and development of the root system in connection with tolerance to drought: roothair defective (rth1-rth3, rth5), absence of seminal root (asr1), bilateral coleoptile (blc1), large primary root (lpr1) lateral rootless (lrt1), root-cap periphery (rcp1, rcp2), rootless (rt1), rootless concerning crown and seminal roots (rtcs1), short lateral root (slr1, slr2), lateral root primordia like (srs1-srs8) and others. The polymorphism of certain genes in these regions is evaluated, design of primers to polymorphic sites is developed, polymerase chain reaction (PCR) in silico is performed. The developed primer pairs are used for PCR in vitro to analyse a molecular genetic polymorphism of maize genotypes differing in degree of drought tolerance.