Aims: To identify and quantify the presence of Escherichia coli, Staphylococcus aureus, Salmonella, hepatitis A and norovirus in households and to assess the effect of chlorine and quaternary ammonium-based disinfectants following a prescribed use. Methods and Results: Eleven sites distributed in kitchen, bathroom, pet and children's areas of two groups of 30 homes each: (i) a nonprescribed disinfectant user group and (ii) a disinfectant protocol user group. During the 6-week study, samples were collected once a week except for week one when sample collection occurred immediately before and after disinfectant application to evaluate the disinfectant protocol. The concentration and occurrence of bacteria were less in the households with prescribed use of disinfectants. The greatest reductions were for E. coli (99%) and Staph. aureus (99.9999%), respectively. Only two samples were positive for HAV, while norovirus was absent. Disinfection protocols resulted in a significant (P < 0.05) microbial reduction in all areas of the homes tested compared to homes not using a prescribed protocol. Conclusions: The study suggests that disinfectant product application under specific protocol is necessary to achieve greater microbial reductions. Significance and Impact of the Study: Prescribed protocols constitute an important tool to reduce the occurrence of potential disease-causing microorganisms in households.