The relationship between chemical structure and antimicrobial activity of 201 quaternary imidazolium compounds is analysed using the theory of rough sets. The compounds are described by 8 attributes concerning structure and are divided into 5 classes of activity. The description builds up on information system. Using the rough sets approach, first a minimum set of 4 attributes significant for a high quality of classification has been found. The analysis of distribution of values of significant attributes in the best and worst class led to the definition of typical representatives of best and worst compounds in terms of significant attributes. Finally, a decision algorithm has been driven from information system, showing important relations between structure and activity. It may be helpful in supporting decisions concerning the synthesis of new antimicrobial compounds.