In order to prevent or reduce environmental and public health damages, is essential to control the microbiological quality of wastewater used in irrigation. Traditionally faecal and total coliforms are use to accomplish such control, and in countries with there is a high incidence of gastrointestinal diseases of parasitic origin, helminth eggs count is done, With improvement in diagnostic methods and the application of epidemiological and microbiological tools, the scenery of sanitary risk has changed introducing new elements for analysis and discussion. Some of these changes are related with the type of microorganisms to be control, the concentration limits to be allowed, the crop type, population exposed and environmental and health circumstances of each country. The World Health Organization suggests continuing with the evaluation of faecal coliforms and helminth eggs. However, discussion continues for the use of indicators that weighs up virus, protozoa, and emergent micro organisms that not always can be evaluated with traditional indicators.