Soybean cyst nematode (Heterodera glycines) is a major yield limiting pest in all major soybean producing countries. In the last decade genetically modified soybean tolerant to glyphosate has become widely planted and postemergence application of glyphosate has increased exponentially. Genetically modified crops may affect nontarget microorganisms, either directly or indirectly as in the case of glyphosate application to tolerant crops. Glyphosate translocates to soybean roots where it might affect metabolic sinks such as syncytia produced by Heterodera glycines. In 2002 - 2004 glyphosate tolerant soybean DSR 320 susceptible to H. glycines and DSR 327 resistant to H. glycines were grown in three different fields and either sprayed with glyphosate at the recommended rate and time of application or not sprayed. Nematode reproduction and soybean yield were determined. In all three years, Pf and Pf/Pi were significantly greater on DSR 320 when compared with DSR 327. In 2004, when Pi exceeded the damage threshold, there was a cultivar × glyphosate interaction for Pf on DSR 320 with greater numbers of eggs recovered from glyphosate treated DSR 320. In 2002 and 2003 Pi was below the damage threshold and no differences in yield occurred between the resistant and susceptible cultivars. However, in 2003 a significant cultivar × glyphosate interaction was observed for yield of DSR 320. In 2004 a significant difference in yield between DSR 320 and DSR 327 was observed. Glyphosate application affected Pf of H. glycines eggs in 2004, the only year Pi exceeded the damage threshold. However, the increase Pf did not translate into crop loss.