A total of 150 samples of Oreochromis niloticus were collected during summer season of 2011 from different intensive farms previously known be infected and treated by disinfectant at Kafr El-Sheikh, Governorate. The samples were assessed for the determination of malachite green residual levels in fresh, scalded (boiled) and microwave by HPLC. Malachite green residues not detected in 81.33% (122) of the examined Oreochromis niloticus samples. The mean concentrations of the malachite green residual level in the fresh Oreochromis niloticus muscle was 2.20 ± 0.50 ppb. On study of the effect of thermal processing, the reduction percentage in the levels of malachite green in the scalding (boiling) and microwave treated samples were 52.51% and 59.98% respectively. From the sum of the examined fresh Oreochromis niloticus samples 81.33% (122) were agree with the permissible limit established by FDA for malachite green, while 18.66% (28) of the fresh samples that treated by scalding (boiling) and microwave exceeded the permissible limit. This indicates that cooking by scalding (boiling) and microwave reduces the level of malachite green but not removed it from fish muscle. The relationship between the levels of malachite green in fresh, scalding and microwave treated samples as well as the public health significance of these residues were discussed.