Aside from antiviral treatment and the pandemic influenza A (H1N1) 2009 virus vaccine the role of which is indispensable in an influenza pandemic, the use of hygiene measures within school premises has a critical role in the delay of the evolution of the pandemic with concomitant reduction of serious illness and deaths, and societal disruption among citizens. Influenza A (H1N1) 2009 shares the same mode of transmission, spectrum of clinical presentations, surveillance case definitions, and infectious period with seasonal influenza while severe disease occurs mainly in individuals with known risk factors, and more than seasonal influenza in the 5-55 year old age group. School-aged children are not in the high priority groups for immunization against influenza A/H1N1 2009 vaccine as of yet. The epidemiology of the current pandemic in schools is presented, followed by a review of the literature regarding the hygiene measures in schools, from Kindergarten to the 12th year of education in high school, grouped into those applied on individual base, environmental cleaning and ventilation, reporting and outbreak recommendations, selective school closure, and a stricter version of these should a pandemic with more severe circumstances emerges during the 2009-2010 flu period. Respiratory etiquette, alternate use of elbow for younger children, avoidance of sharing of cups, and eating utensils, correct hand washing technique being the exclusive method when hands visibly soiled, and alcohol based hand rubs safely disposed of, monitoring of children and staff, isolation in separate room when symptomatic at school, and at home despite use of antivirals, constitute the individual base hygiene measures, while routine disinfection of contaminated surfaces at least daily, and the good ventilation constitute the environmental precautions. Instead, official sick leave and return to school documentation and personal protected equipment are not indicated in school setting. Recording and reporting of cases of ILI and above expected levels absenteeism, should be subsided by a multidisciplinary forum convention under the coordination of local public health in order that selective school closure and the less costly class suspensions are decided timely. Students should be discouraged to congregate elsewhere and reduce the benefit from selective school closure. The conclusions derived from the measures taken in affected countries since April 2009, historical data from 1918-1919 pandemic and simulation studies are: (i) Reactive school closure as a result of school absenteeism and/or staff shortages, should more severe circumstances of this pandemic emerge, will be acceptable by the public. (ii) Proactive closure implemented early before severe illness occurs in the community to decrease the spread of flu, will not be widely acceptable, unless, under circumstances of severe disease, delineation of authority among all relevant stakeholders and transparent communication between Public Health officials and population exist. (iii) Selective school closure is indicated under current circumstances. School operation is considered to have optimal impact on the pandemic evolution as it educates children and families about this, supports the economy and social infrastructures allowing parents to work, and provides the structured environment for the efficient administration of vaccines to this highly important age group of the community. (iv) Sanitary measures are characterized by a transient protective nature and their use should be sustained. This pandemic sets their role as indispensable and provides an exercise for strict and sustained implementation of hygiene measures, the importance of which, was relatively underestimated in schools, after the laudable advances of Medicine and Health during last century.