Rhizomania is one of the most destructive and damaging sugar beet diseases that has spread in different regions of Iran. In order to evaluate the genotypic, environmental, and genotype by environmental variability of sugar beet genotypes under rhizomania infection, variance components were estimated from the trial series in 7 years. Required data, such as yield and quality parameters, were collected from value for cultivation and use trials. Results of analysis of variance showed that the environment was the source that explained most of the variability, except for amino‐N and alkalinity. Quality traits were also influenced by the environment × cultivar interaction, so that 4.8% (white sugar content) to 46.1% (alkalinity) variance was observed. In contrast, genetic variation was much lower, between 1.2% (potassium) and 27.4% (amino‐N). A strong and negative correlation was found between root yield, sugar yield, and white sugar content with the disease index, which obviously illustrates the negative impact of the rhizomania on root weight and as a consequence on the dependent traits. The cluster analysis of the cultivars based on the quantitative and qualitative traits and the disease index showed that the range of variation in traits, such as the disease index, varied from 6.25 for the susceptible cultivar to 1.25 for the resistant one. This indicates the existence of sufficient genetic diversity among cultivars in terms of this trait. High impurity accumulation was observed in Shiraz region compared with Mashhad. In conclusion, it is observed that rhizomania has a significant effect on the impurity concentration in the root, especially sodium, potassium, and amino‐N. This is very important in the sugar industry because sugar extraction depends on the concentration of these impurities, in addition to the sugar content of each cultivar.