Hexabromocyclododecane (HBCD), a brominated flame retardant, has become a ubiquitous contaminant due to its wide application, persistence, and toxicity. HBCD diastereoisomers have different physical and chemical properties and may differ in their bioaccumulation and toxicity in plants. Accumulation and toxicity of α-, β-, and γ-HBCDs in maize were investigated in the present study. The accumulation was in the order β-HBCD > α-HBCD > γ-HBCD in roots and β-HBCD > γ-HBCD > α-HBCD in shoots. Both the inhibitory effect of the diastereoisomers on the early development of maize and the intensities of hydroxyl radical and histone H2AX phosphorylation in maize exposed to 2 μg L −1 HBCD followed the order α-HBCD > β-HBCD > γ-HBCD, indicating the diastereomer-specific oxidative stress and DNA damage in maize. It was further confirmed that the generation of reactive oxygen species was one, but not the only, mechanism for DNA damage in maize exposed to HBCDs.