Abstract: The selection of ground motion input is one of the key procedures in the analysis of structural collapse fragility, but its impact on the uncertainty is usually ignored. The strong motion records from PEER database are divided into 9 groups by constraining the range of a single variable, which is one of the earthquake magnitude, distance and site parameters (M, R, V_S30). A new index I_Sa is proposed to evaluate the difference of the relative energy of different groups of strong motion records. Incremental dynamic analysis (IDA) is conducted to analyze the collapse fragilities of three concrete frame structures, which are 3-floor, 8-floor and 15-floor with different natural periods, respectively. The fragilities derived from each group of the ground motion inputs are compared. They are also compared with the fragilities when the 22 records recommended by ATC63 are used as the ground motion inputs. The results show that the ground motion intensity representing the occurrence of collapse performance S_a(T₁) decreases with the increase of earthquake magnitude, increase of epicentral distance and decrease of V_S30, irrespective of the structures of concern. All three structures are more vulnerable to collapse if the strong-motion records at a far-field soft site in a large earthquake are selected as the seismic inputs, which is approximately consistent with the distribution of the relative energy of the ground motions represented by I_Sa. The comparisons of the two parameters SI and SI_max among the different groups indicate that there is a relatively high sensitivity of epicentral distance for long-period structures, and the structural collapse fragility is more sensitive to the earthquake magnitude than to either the distance or the site condition. It is confirmed that a large uncertainty of the structural collapse fragility will be produced if the 22 records recommended by ATC63 are used as the ground motion inputs. For the sake of decreasing the uncertainty, it is suggested to use a method which can consider the seismic hazard of the site and the structural dynamic characteristics to select appropriate ground motion inputs when analyzing the collapse fragility of a structure.