Soil nematodes and bacteria play an important role in soil function. In order to evaluatethe effects of agricultural practices on these organisms, a study was conducted in winter wheat fields of Shirvan, Mashhad and Gonabad, three regions of Khorasan Province. In each region, high and low input fields of winter wheat were selected, along with a natural system for comparison. Use of agricultural inputs was the criterion for the selection of low and high input fields in each region. Soil sampling was undertaken on fields and natural systems. Organic matter and the number of nematodes and culturable bacteria in soil samples were measured. The percentage of soil organic matter in all systems was low but, in agro-ecosystems, it was greater than in natural systems. Results showed that organic matter, soil moisture and mean annual temperature has an affect on soil nematodes. The number of nematodes in agro-ecosystems was reater than in natural systems in all three regions. The mean number of soil nematodes in 100g dry weight of soil in the natural systems of Shirvan, Mashhad and Gonabad was 166, 184 and 132, respectively; in the low input systems of Shirvan, Mashhad and Gonabad it was 550, 459 and 1067, respectively and in the high input systems of Shirvan, Mashhad and Gonabad it was 348, 1084 and 485, respectively. Agricultural practices had no negative effects on soil bacterial numbers and the number of soil bacteria increased in some agro-ecosystems. Results showed that agro-ecosystems improved the conditions for nematodes and bacteria and increased the number of these organisms in soil.