Abstract. Late time synthetic spectra of type Ia supernovae, based on three-dimensional deflagration models, are presented. We mainly focus on one model, "c3_3d_256_10s", for which the hydrodynamics (Röpke 2005, A&A, 432, 969) and nucleosynthesis (Travaglio et al. 2004(Travaglio et al. , A&A, 425, 1029 was calculated up to the homologous phase of the explosion. Other models with different ignition conditions and different resolution are also briefly discussed. The synthetic spectra are compared to observed late time spectra. We find that while the model spectra after 300 to 500 days show a good agreement with the observed Fe II-III features, they also show too strong O I and C I lines compared to the observed late time spectra. The oxygen and carbon emission originates from the low-velocity unburned material in the central regions of these models. To get agreement between the models and observations we find that only a small mass of unburned material may be left in the center after the explosion. This may be a problem for pure deflagration models, although improved initial conditions, as well as higher resolution decrease the discrepancy. The relative intensity from the different ionization stages of iron is sensitive to the density of the emitting iron-rich material. We find that clumping, with the presence of low density regions, is needed to reproduce the observed iron emission, especially in the range between 4000 and 6000 Å. Both temperature and ionization depend sensitively on density, abundances and radioactive content. This work therefore illustrates the importance of including the inhomogeneous nature of realistic three-dimensional explosion models. We briefly discuss the implications of the spectral modeling for the nature of the explosion.