The aim of this study was to investigate the toxic effects of different doses of Paraquat treatment on Allium cepa L. Root length (RL), germination percentage (GP), weight gain (WG), chromosomal aberrations (CAs), micronucleus (MN) frequency and anatomical alterations (AA) were used as toxicity indicators, and the data were correlated with statistical parameters. The seeds were seperated into four groups; one as control and three as Paraquat treatment groups. Paraquat doses of 10, 50, and 100ppm were used in treatment groups during 72h. The results indicated that Paraquat showed dose-dependent effects in the RL, GP, WG, CAs, MN frequency and AA on Allium cepa L. seeds. Increasing the dose of Paraquat significantly decreased RL, WG and GP in all of the treatment groups. The highest rate for RL, GP and WG were observed in the control group. Also, the frequency of MN and CAs showed dose-dependent increase in all of the Paraquat treatment groups. The rate of MN formation and CAs frequency were observed to be highest at the 100-ppm dose of Paraquat and lowest at the 10-ppm dose of Paraquat. Paraquat treatment caused anatomical alterations on root tips and rate of anatomical alterations increased with increasing dose of Paraquat. The results of this study showed that the widely used Paraquat herbicide showed toxic effects at certain concentrations which was demonstrated using Allium cepa L. test material. The selected parameters such as RL, GP, WG, CAs, MN frequency and AA are very sensitive and useful biomarkers for bio-monitoring these effects.