In the present study, 40 juvenile crucian carp (Carassius auratus) were caught from a river close to an electronic waste (e-waste) site (exposed group) and another located 80 km away from the e-waste site (control group) in Zhejiang, China. Results indicated that muscle levels of polybrominated diphenyl ethers (median PBDEs, 235.98 ng/g wet wt; range, 7.70-703.31 ng/g wet wt), serum levels of thyroid-stimulating hormone (median TSH, 2.32 µIU/ml; range, 2.05-2.72 µIU/ml) and erythrocyte DNA damage level (median Olive tail movement, 16.27 µm; range, 4.28-27.51 µm) were higher in the exposed group than those in the control group (0.56 ng/g wet wt, range, 0.34-1.24 ng/g wet wt, p < 0.01; 1.70 µIU/ml, range, 1.40-2.08 µIU/ ml, p < 0.01; 6.06 µm, range, 2.01-10.72 µm, p < 0.01, respectively). Thyroxine (T4) was significantly lower in the exposed group (8.97 µIU/ml) than in the control group (12.47 µIU/ml). In addition, thyroid endocrine disorder and erythrocyte DNA damage levels were significantly associated with polybrominated diphenyl ether exposure. Hence, PBDEs may affect wild fish populations in real ecosystems with thyroid endocrine disruption and DNA damage.