Investigations related with factors influencing root and crown rot are rare and mainly related to farming practice and soil management. The main objective of this study was to examine broader range of factors influencing stem-base infestation of winter wheat in the field conditions. The effect of spatial distribution of infected plants on disease index (DIs) assessments was also investigated. Analysis of factors influencing DIs of crown rot of wheat demonstrated significant influence of the growing seasons (P < 0.001) and extreme fluctuations in winter temperatures (P < 0.001). In addition to that, localities together with their interaction with the growing season also significantly influenced DIs (P < 0.001). Aggregation of infected plants influenced variability of DI estimations, and it was pointed out that more extensive investigation should be conducted on broad range of DI in order to establish sampling method giving uniform sampling precision. Fusarium graminearum was shown to be predominant Fusarium species in Serbia (72.6%) using sequence-characterized amplified region analysis. Interestingly F. oxysporum was isolated in higher frequencies (27.4%) than it was reported in the literature. Given that there were no reports on the diversity of Fusarium species causing crown rot of wheat in Serbia, this study presents first report on this important subject. It also indicated that more attention should be focused on combined effects of abiotic and biotic factors influencing stem-base infestation of winter wheat. This knowledge will contribute to better understanding of factors influencing root and crown rot of wheat which would ensure sustainable disease management in the future.