In order to evaluate the effect of freezing stress on electrolyte leakage of three Mooseers’ (Allium altissimum Regel.) ecotypes (Shirvan, Kalat and Tandoureh), a factorial experiment based on completely randomized design with three replications was carried out under the controlled conditions in the Faculty of Agricultural, Ferdowsi University of Mashhad, Iran, during 2009. Plants were grown in natural conditions to acclimate with the growth condition, and then at two growth stages of emergence and seedling were transferred to the thermogradiant freezer with the six freezing temperatures (0,-4, -8,-12, -16 and -20 oC). Cell membrane integrity was measured by electrolyte leakage (EL) index and the lethal temperature 50% (LT50) of samples were determined based on this index. The results showed that electrolyte leakage percentage and LT50el were significantly affected by experimental treatments. As the temperature decreased, EL (%) of leaf, bulb and root of all ecotypes was significantly increased. In the all freezing temperatures, the highest and the lowest electrolyte leakage was observed in the root and leaf in the emergence stage. Shirvan ecotype at two growth stage (emergence and seedling) showed the highest root electrolyte leakage and hence showed the lowest freezing tolerance in comparison with Kalat and Tandoreh ecotypes. The lowest and highest LT50el due to freezing were observed in Kalat, Tandoureh ecotype and Shirvan ecotype, respectively. At seedling stage, Shirvan ecotype’s root showed the highest LT50el which was more sensitive to freezing temperatures in comparison with leaf and bulb. Among all ecotypes, Kalat and Tandoreh ecotypes showed the lowest electrolyte leakage percentage, the lowest LT50el and the most tolerance to the freezing stress.