Hybrid seed corn costs rose from about $35.00/acre in 1998 to more than $100.00 by 2010 primarily because of genetic modification with multiple traits for both insect and herbicide resistance, known as gene stacking. This study compared costs, yields, net returns per acre, and yield components for ten hybrids (four stacked-gene, four glyphosate-tolerant, and two non-genetically modified organisms [GMO]) in a 2-year, furrow irrigated experiment at Stoneville, MS. The site was a Tunica clay (clayey over loamy, smectitic, nonacid, thermic Vertic Haplaquept). The stacked-gene, glyphosate-tolerant, and non-GMO hybrids did not differ in input costs, yield, or net returns per acre within a year. Yields and net returns were greater in 2011 than 2012. Drought during May and two later prolonged cloudy periods in 2012 contributed to lower stands (a reduction of 2500 plants/acre) and fewer kernels per plant (533 vs. 292 for 2011 and 2012, respectively), which reduced yields (∼25%) and net returns (∼50%) compared with 2011. Non-GMO hybrids had yields and net returns similar to most stacked-gene hybrids both years when insect pressure was negligible and postemergence weed control was unnecessary. Production of some non-GMO hybrids requiring preemergence herbicides should help protect against glyphosate-resistant weeds and sustain the insect resistance of Bt genotypes by providing a refuge without an economic penalty.