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The production of pearl millet [Pennisetumn glaucum (L.) R. Br.] in the low fertility sandy soils of the Sahel region of northern sub-Saharan Africa requires careful management. An experiment was established in 1993 at the Niamey Center of the International Crops Research Institute for the Semi-Arid Tropics, Niger. The objectives were to (i)determine the effect of long-term applications of fertilizer, crop residue, cattle manure, and combinations of these on changes in grain yield (GY) and total dry matter (TDM) of pearl millet; (ii) determine the effect of management on nitrogen application efficiency (NAE) and nitrogen use efficiency (NUE), using data from 1998 and also from 2005 and 2006. Fertilizer use showed significant positive effects on GY and TDM from 1998 to 2006. The positive effects of organic matter appeared rather later, that is, around 8 yr after the start of the experiment. The GY and TDM were strongly affected by N and P but not K. From 1998 to 2000, N-fertilizer strongly affected GY and TDM, but TDM increased gradually with the total amount N application, including N from organic matter. Nitrogen uptake by pearl millet was similar among treatments except for control in 2005, but in 2006 was higher in the treatments that combined fertilizer and organic matter. The NAE in combined applications of fertilizer and crop residue, and NUE in the treatments with residue showed higher trends than other treatments. This suggested that residue had more potential than cattle manure to enhance the effect of fertilizer.