Organic farming systems require different production methods than conventional farming systems. Plant breeding programs typically select varieties within a conventional farming system that incorporates the use of inorganic nitrogen fertilizer and crop protection chemicals, practices not permitted under organic farming standards. The objective of this study is to answer the question: Are the highest yielding varieties in conventional systems also the highest yielding in organic systems? To address this objective, we quantified the overall differences in yield of winter wheat when grown under two contrasting systems, organic and conventional. Thirty-five advanced winter wheat breeding lines (F6 to F9) were evaluated for yield in split-plot, randomized complete block (RCB) experiments at five locations over two years in Washington State. Main plots were organic and conventional wheat breeding nurseries. Preliminary data for the 35 breeding lines showed significant genotype x system interactions within each location. Genetic correlation coefficient (rG) was calculated to estimate genetic independence between both systems. The estimates of rG indicate that alleles responsible for high yields in both organic and conventional systems are moderately to highly independent between systems. These results support the hypothesis that varieties for organic agriculture should be selected within an organic production system to achieve maximum yield potential. To decompose the sources of the total variation between organic and conventional systems, we established split-plot, RCB competition nurseries to determine the effect of weed pressure and mechanical cultivation on wheat varieties. Wheat varieties were measured for weed suppression ability, weed tolerance and harrow tolerance. Preliminary results suggest that weed pressure contributes significantly to the variation between organic and conventional systems and that wheat varieties can be selected for improved weed competitive ability. Other sources of variation between organic and conventional farming systems, including disease pressure and nitrogen use efficiency, are currently being investigated.