Biocides have been in use for hundreds of years for antisepsis, disinfection and preservation. Despite this widespread and ever increasing use most bacterial and fungal species remain susceptible to biocides. The dramatic increase and spread of resistance to antibiotics linked to reports of co- and cross-resistance between antibiotics and biocides raised speculations on potential hazard of biocide use. The overarching question which BIOHYPO is aimed to address is: has the use of biocides contributed to the development and spread of clinically significant antibiotic resistance in human pathogens? Core of BIOHYPO are a high throughput screening approach on collections of thousands of well characterized microorganisms and an interactive web based data analysis platform. Phenotypic screening for reduced susceptibility to biocides, detection of novel resistance genes and mobile elements, and screening for their molecular epidemiology and metagenomics will be accompanied by methodological innovation for testing, risk evaluation and registration of biocides. Altogether BIOHYPO aims to provide solid data and analysis to direct future issuing of guidelines for safe environmental, medical and industrial use of biocides.