PACS 68.37. Lp, 79.20.Uv, 81.05.Bx, 82.80.Ms Thin films of niobium were deposited on thermally oxidized Si-(100)-wafers by two different methods: electron beam evaporation and direct current reactive magnetron sputtering. The thicknesses of asdeposited niobium films were 200 and 500 nm. 200 nm evaporated niobium films were nitridated in nitrogen and ammonia using rapid thermal processing (RTP). In these investigations the reactivity of N 2 and NH 3 with Nb-films was compared. 500 nm sputtered Nb-films were annealed in several steps. At first niobium films were nitridated under ammonia atmosphere at 1000 °C for 1 min using an RTP. After that nitridated niobium films were oxidized in molecular oxygen at temperatures ranging from 400 to 600 °C. Before and after reactions with ammonia, oxygen and nitrogen evaporated and sputtered samples were characterized by several complementary analytical methods. X-ray diffraction (XRD) was used for phase analysis after annealing. Determination of the elemental depth profiles of the films was realized by secondary ion mass spectrometry (SIMS). Microstructure and spatial distribution of the elements were imaged by transmission electron microscopy (TEM) and energy-filtered TEM (EFTEM). Electron energy loss spectra (EELS) were taken at selected positions to discriminate between different nitride, oxynitride and oxide phases. Investigation by scanning electron microscopy (SEM) and atomic force microscopy (AFM) revealed differences of the film morphology depending on the reactive agent and reaction temperature. Investigations of sputtered films show that surface roughness of the samples after oxidation of niobium films nitridated in ammonia before is lower then after direct oxidation of as deposited films in oxygen, in spite of the same phase of niobium pentoxide formed after annealing in both cases. We explain this due to large expansion of niobium lattice during direct oxidation of Nb-film in molecular oxygen. By incorporation of oxygen in the crystal lattice of niobium and formation of niobium pentoxide substantial intrinsic stress was built up in the film frequently resulting in delamination of the film from the substrate. The possibility of the formation of niobium oxynitride phase after three steps annealing in ammonia, oxygen and finally in ammonia was investigated.