To integrate conventional and marker-assisted breeding for downy mildew (Sclerospora graminicola) resistance in pearl millet (Pennisetum glaucum), a backcrossing program was intitiated at ICRISAT-Patancheru using conventional greenhouse screening to introgress previously mapped downy mildew resistance QTLs of large effect from donor parent IP 18293 into genetic backgrounds of susceptible elite inbreds 81B and 843B. During 2004 we assessed 68 BC1F2/BC2F1 progeny pairs for recurrent parent 843B, and 39 BC1F2/BC2F1 progeny pairs for recurrent parent 81B, against a downy mildew pathogen population from IARI, New Delhi, in three replications under severe seedling greenhouse screening conditions. Pathogen population choice was based upon prior QTL mapping results. Downy mildew incidence (DMI) on donor parent IP 18293 was 1%, compared to 48% and 92% on recurrent parents 81B and 843B, respectively. Comparison of DMI values for individual BC1F2/BC2F1 progeny pairs with parental values and expected Mendelian segregation patterns allowed identification of BC2F1 progenies likely to carry one, two or three additional major DM resistance genes from the donor in more elite genetic backgrounds. Selected BC2F1 progenies were advanced by selfing and backcrossing to produce BC2F2/BC3F1 progeny pairs for the next screening cycle. Single R-gene introgression lines bred by this method can be used as near-isogenic differential lines to characterize pathogen variability. Multiple R-gene introgression lines bred by this procedure may find use as more downy mildew resistant replacements for 81B and 843B. Where facilities for controlled screening of potted seedlings with an appropriate pathogen isolate are available, this high-throughput mapping-directed conventional screening procedure is more rapid and less expensive than RFLP-based marker-assisted selection, while still tracking segregation of individual resistance genes. This should facilitate implementation of resistance gene deployment strategies for pearl millet downy mildew.