A comparative study was conducted on the start-up performance and biofilm development in two different biofilm reactors with aim of obtaining partial nitritation. The reactors were both operated under oxygen limited conditions, but differed in geometry. While substrates (O2, NH3) co-diffused in one geometry, they counter-diffused in the other. Mathematical simulations of these two geometries were implemented in two 1-D multispecies biofilm models using the AQUASIM software. Sensitivity analysis results showed that the oxygen mass transfer coefficient (Ki) and maximum specific growth rate of ammonia-oxidizing (AOB) and nitrite-oxidizing bacteria (NOB) were the determinant parameters in nitrogen conversion simulations. The modeling simulations demonstrated that Ki had stronger effects on nitrogen conversion at lower (0-10 m d(-1)) than at the higher values (>10 m d(-1)). The experimental results showed that the counter-diffusion biofilms developed faster and attained a larger maximum biofilm thickness than the co-diffusion biofilms. Under oxygen limited condition (DO<0.1 mg L(-1)) and high pH (8.0-8.3), nitrite accumulation was triggered more significantly in co-diffusion than counter-diffusion biofilms by increasing the applied ammonia loading from 0.21 to 0.78 g NH4+-NL(-1) d(-1). The co- and counter-diffusion biofilms displayed very different spatial structures and population distributions after 120 days of operation. AOB were dominant throughout the biofilm depth in co-diffusion biofilms, while the counter-diffusion biofilms presented a stratified structure with an abundance of AOB and NOB at the base and putative heterotrophs at the surface of the biofilm, respectively.