Abstract. We study the effects of the interaction of 40-fs Ti-sapphire laser radiation at 800 nm with biological materials-proteins or intact Bacillus spore, dissolved or suspended in pure water, respectively. The estimated laser intensity at the target is 10 13 W∕cm 2 . On the molecular level, oxidation of solvent-accessible parts of proteins has been observed even after a single femtosecond laser pulse, as demonstrated by mass spectrometry. A remarkable morphological effect of the femtosecond laser radiation is the complete disintegration of extremely refractive cells such as bacterial spores, evidenced in scanning electron micrographs. After 500 laser pulses, all suspended spores in the irradiated volume are completely destroyed, which makes them nonviable. Characteristic spore biomolecules, e.g., small acid-soluble spore proteins, are extensively oxidized after several laser pulses. In comparative studies, no effects have been observed when irradiating the same samples with 10-ns laser pulses at the same laser wavelength and fluence. We demonstrate that the laser power density (irradiance), resulting in different amounts of total deposited energy, determines the types of effects for femtosecond laser interactions with biological matter. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.