An evaluation of the efficacy of the use of either formaldehyde (10% formalin) or peroxygen commercial products in disinfection of battery cage poultry houses was estimated under field conditions. For this purpose, swab samples were collected from three different sites and from drinking water dispensers from four battery caged broiler and layer houses before and after cleaning and disinfection. Also, water samples were collected from the original well water source and the storage water tanks (main and houses storage water tanks) before cleaning and disinfection. Total colony counting was used in the evaluation of both swabs and water samples followed by bacteriological examination for identifying the contaminant bacteria.  The results of the examination of water samples revealed that in spite of sterility of original water source there was sever contamination of the stored water in the storage tanks with different types of pathogenic contaminant bacteria including Staphylococcus aureus, E.coli, coliforms, Pseudomonas earuginosa and Proteus spp.. The same contaminant bacteria were isolated from the swab samples in addition to salmonella typhymiurium contamination which was isolated from batteries and floors of both broiler and layer houses. On the other hand, both the tested disinfectant products were significantly effective (p < 0.001) in decline the viable total colony count from different sites of each house and from drinking water dispensers from either broiler or layer cage houses with depletion percentage reached 99.999% but the use of formaldehyde product failed to overcome the pathogenic contaminant bacteria except for salmonella typhymiurium contamination. The efficiency of the disinfection was more effective in broiler houses than in the layer ones. On conclusion, a high standard planning of cleaning is of great importance before the application of the disinfection process and the correct usage of disinfectants in addition to, an effective program of eradication of rodents and insects should be applied is important for a successful disinfection and biosecurity program. Also, the obtained data highlights the emergence of the necessity of improving farmers' and hygiene specialists' education on the use of disinfecting products in poultry houses. It was recommended to use more environmental friendly safe and efficient disinfectants as peroxygens to be alternative to the use of formaldehyde in disinfection of poultry houses which may soon become illegal in some countries due to its health hazard and environmental concerns.