Redox enzyme - glucose oxidase E.C. 1.1.3.4 from Penecillum vitale (GOx) - initiated polypyrrole (Ppy) synthesis was applied for the formation of polypyrrole based nanoparticles. The increase in optical absorbance at lambda=460 nm was exploited for the monitoring of polypyrrole polymerisation process. The shape and size of the formed Ppy nanoparticles was also monitored by means of contact mode AFM. The highest increase in the diameter of the formed Ppy nanoparticles was detected during 15-day period. AFM imaging was performed in contact mode to investigate the shape and flexibility of particles deposited on the SiO2 and Pt surfaces. Contact mode AFM investigations allowed us to conclude that after drying at 50 degrees C the formed Ppy particles are more flexibly deposited on the Pt electrode if compared to those deposited on the SiO2 substrate. The application of well-shaped Ppy nanoparticles in biomedicine, chromatography and bioanalysis may be predicted.