A reporter system for ФC31 integrase was developed in NIH3T3 cells. The reporter plasmid coding green fluorescent protein (GFP) coupled with red fluorescent protein (RFP) was co-transfected with the plasmid coding ФC31 integrase, to show the activity of integrase in the cells. Fluorescence activated cell sorter (FACS) was used to measure the proportion of the cells containing red and green fluorescence. The increment of green cells was positively related to the increase in the transfection with plasmid coding ФC31 integrase. Approximately 90% of green cells were observed under a ratio of [plasmid-ФC31-integrase]/[reporter plasmid] at 10∶1. This suggests that the ФC31 integrase reporter system provides a probe for the function of ФC31 integrase in cells.