Coastal sea circulation models are a useful tool for sea forecasting and a good starting point for calculating pollutant transport. Two similar three-dimensional baroclinic hydrodynamic models (PCFLOW3D and MIKE3) were compared on a case study of the Gulf of Trieste. The comparison was not based only on the graphic (visual) parameters, but was also numerically evaluated using the normalised root-mean-square deviation method (RMSDN). Typical cases of circulation were selected, where the similarities and differences between both models are clearly visible. Density-driven flows were studied, as well as the impact of strong wind (bora), mild wind (maestral) and the tide on circulation. In one case, constant coefficients of turbulent viscosity in the horizontal and vertical directions were used. In this case the results show dependence on the different numerical schemes and on the definition of boundary conditions of both models. In all other cases, the turbulence models used were as similar as possible, selected among the ones usually used in circulation models (Smagorinsky in the horizontal direction in both models and in the vertical direction k-є and Mellor-Yamada in MIKE3 and PCFLOW3D, respectively). An additional comparison with refined grid was performed in the events of density-driven flow and strong bora wind in the area of the Soča river inflow. The results of both models are similar. However, there are noticeable local discrepancies due to the differences between the models, mostly the different turbulence models and the boundary conditions definition. The results were also compared to simulations performed by the POM model. This three-way comparison showed in general a very similar picture of circulation. According to the results, both models, MIKE3 and PCFLOW3D, can be used interchangeably in areas with characteristics similar to the Gulf of Trieste.