The objective of the study was to analyze and compare fatigue properties of composites based on two biodegradable polymers: thermoplastic starch and polylactide blend filled with 10 wt% short flax fibers. Accelerated fatigue tests with increasing amplitude were done on neat polymers and their composites. Dissipated energy, strain and the temperature on the sample surface were the three characteristic values measured or calculated during the tests to evaluate fatigue stress of the materials with the use of Lehr's method. The increase in temperature was not observed. Addition of flax fibers resulted in improvement of fatigue strength of polylactide-based composite but thermoplastic starch filled with flax fibers showed lower fatigue strength than neat polymer, shortened fatigue life and higher susceptibility to cyclic creep.