Wheat (Triticum aestivum L.) varieties produced using modern biotechnologies, such as genetic engineering and mutagenic techniques, have lagged behind other crop species, but are now being developed and, in the case of mutagenic wheat, commercially grown around the world. Because these wheat varieties have emerged recently, there is a unique opportunity to assess comparatively the potential environmental risks (human health, ecological, and livestock risks) associated with genetically engineered, mutagenic, and conventional wheat production systems. Replacement of traditional herbicides with glyphosate in a glyphosate-tolerant (genetically engineered) wheat system or imazamox in an imidazolinone-tolerant (mutagenic) wheat system may alter environmental risks associated with weed management. Additionally, because both systems rely on plants that express novel proteins, the proteins and plants themselves may impose risks. The purpose of our study was to examine comparatively the multiple aspects of risk associated with different wheat production systems in the US and Canada using the risk assessment paradigm. Specifically, we used tier 1 quantitative and qualitative risk assessment methods to compare specific environmental risks associated with the different wheat production systems. Both glyphosate and imazamox present lower human health and ecological risks than many other herbicides associated with conventional wheat production systems evaluated in this study. The differences in risks were most pronounced when comparing glyphosate and imazamox to herbicides currently with substantial market share. Current weight-of-evidence suggests that the transgenic CP4 EPSPS protein present in glyphosate-tolerant wheat poses negligible risk to humans, livestock, and wildlife. Risk for mutated AHAS protein in imidazolinone-tolerant wheat most likely would be low, but there are not sufficient effect and exposure data to adequately characterize risk. Environmental risks for herbicides were more amenable to quantitative assessments than for the transgenic CP4 EPSPS protein and the mutated AHAS protein.