In-duct ultraviolet germicidal irradiation systems are effective systems that are used in disinfection of pathogenic particles transported by air that moving through the ventilation systems. Proper design of these systems is quite important for energy consumption and disinfection performance. In this study, effect of four different lamp arrays within a square cross-section ventilation duct on the average UV dose, UV dose distribution and disinfection rate are examined by using computational fluid dynamics. The standard k-epsilon turbulence model and the discrete phase modeling are used to analyze airflow and particle distribution within the duct, respectively. Also, Discrete Ordinates (DO) radiation model is employed to obtain the irradiation field formed by each UV lamp. It is disclosed that UV lamp arrangement within duct significantly affects UV dose distribution.