Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. Initial analyses of the comprehensive data set showed that beside coding RNAs, known and yet unknown putative novel ncRNAs comprise a significant part of the responses. We also computed a scores for all genes to be used for predictions for their probability to be regulated at certain stresses. The core scores enabled identification of universal stress responders representing conserved gene products involved in basic mechanisms important for responses to multiple stresses. Further, the environmental specific core scores made it possible to predict functions of yet non-characterized and also hypothetical gene products. All data are collected in the PATHOGENEX interactive RNA atlas, which is made available to the research community providing ample opportunities for discovering new aspects of regulatory networks in pathogenic bacteria as well as identification of novel players critical for bacterial infectivity and maintenance of infections. Overall design: Stress response of 32 human bacterial pathogens to 11 infection relevant stress conditions.