We present a method by which the degree of longitudinal variation in photonic crystal fibre (PCF) may be characterised through seeded four-wave mixing (FWM). Using an iterative numerical reconstruction, we created a theoretical model of the PCF that displays FWM phasematching properties that are similar to experiment across all measured length scales. Our results demonstrate that the structure of our PCF varies by less than ±1 % and that the characteristic length of the variations is approximately 15 cm.