The aim of the M. Sc. Thesis was to determine antimicrobial activity of 13 samples of wood fungi and 46 samples of endophytic fungi. The potential antimicrobial activity of the individual extracts was first verified by a microdilution test. From the results obtained, the percentage of inhibition was calculated. The extracts that showed good antimicrobial activity were then analyzed by High-preformance liquid chromatography. The individual fractions were then re-tested on a preliminary microdilution test to determine in which fractions the antimicrobials are found. We wanted to reach an individual compound that has antimicrobial activity and determine its identity by mass spectrometry. We have found that the selected wood fungi do not show antimicrobial activity, and that some endophytic fungi show antimicrobial activity against both Gram-positive (S. aureus) and Gram-negative bacteria (E. coli). It has also been shown that ethanolic extracts of endophytic fungi have a better antimicrobial activity against S. aureus than against E. coli. Based on the screening of extracts of fungi, we have come up with two structures that have great potential as the basis for the development of new antibiotics.