Accumulation of heavy metals and their uptake by different plant parts depend on the concentrations available heavy metals in the soil and form of metals. In the present study the levels of some selected heavy metals (Mn, Zn, Cr, Ni, Cu, Cd and Pb) in onion and irrigation water sampled from selected Woredas of Gurage Zone (i.e.Meskan, Mareko, Sodo, Muhir Aklil and Cheha Woredas), Southern Region, Ethiopia were analyzed. The onion samples were weighed to determine the fresh weight and dried in an oven at 80 oC for 72 hours to determine their dry weight. The dry samples were then grounded in a mortar and the resulting powder digested by weighing 0.5g of oven-dried ground and sieved (<1mm) into an acid-washed porcelain crucible and then incinerated at 500 oC in a muffle furnance. The crucibles were removed from the furnance and cooled. The ashes were then solubilised in concentrated HCl for analysis. The contents of the minerals in the digests were analyzed using flame atomic absorption spectrometer (FAAS). The following concentration ranges (mg/kg) were found in onion: Zn (11.55 - 24.91), Cu (ND – 6.63), Mn(12.23 - 49.22), Cr (ND-54.57), Ni (0.87 - 8.45), Pb and Cd were ND( i.e. Below method detection) in all woreda samples. In this study, all heavy metals were not found (below method detection limit) in water samples. However, levels of heavy metals in onion samples were found in appreciable amount. The level of heavy metals in onions samples determined in this study could be put in the following order Mn > Zn > Cr > Ni > Cu. However, Cd and Pb were not detected in onion samples. The concentrations of heavy metals in onions were found below the permissible limit prescribed by different standards. However, the amount of Cr determined in onion was found above allowable limit recommended by WHO.