Wheat varieties from Turkey, Australia and the Pacific Northwest of the US were screened for resistance to Fusarium crown rot (Fusarium pseudograminearum and Fusarium culmorum) in inoculated growth chamber studies. Fungal DNA was also quantified from the lower stems (crowns) of seedlings using quantitative PCR and crown rot scores were correlated with DNA results. There were significant differences among the varieties for crown rot severity index (p = 0.0265), crown rot score (p = 0.0003), disease index on leaf sheaths (leaf sheath score) (p = 0.0013), lesion length (p = 0.0200), and plant height (p < 0.0001). The crown rot score and plant height measurements also showed that the isolate of F. culmorum was more virulent than the isolate of F. pseudograminearum. The correlations were strongest between crown rot score and DNA levels at the second harvest, and much stronger with the isolate of F. culmorum compared to the isolate of F. pseudograminearum. Some susceptible varieties such as Seri had both a high disease score and high quantities of DNA, with both F. culmorum and F. pseudograminearum. On the other hand, varieties such as Matt, Sunco and Otis showed intermediate to high crown rot scores in response to F. culmorum, but much lower levels of DNA than Seri. 2-49, Burbot-6 and CT000161, in response to F. culmorum, showed low levels of disease and low levels of DNA. In conclusion, there were examples of varieties that were resistant and tolerant (low levels of DNA and disease), resistant and intolerant (low quantities of DNA, but higher levels of disease) and susceptible and intolerant (high quantities of DNA and disease). Quantitative PCR in combination with classical phenotyping of resistance to Fusarium crown rot may provide a tool for distinguishing resistance and tolerance in breeding efforts.