Information on the seismic response of chemical containers located in storage racks is very limited. Unfortunately, no clearly established data and statistics exist related to potential damage of chemical racking systems during earthquakes. Hence, this work presents an approach for developing fragility curves for chemical racking systems in the cross-aisle direction through dynamic non-linear analysis. It aims to simulate the structural behaviour of various racking systems in the cross-aisle direction for the worst-case scenario, in order to quantify the vulnerability of chemical racks in seismic areas and to better understand the associated natech risk. Analytical fragility curves and a fault tree model were derived and used to evaluate the probabilities of chemical containers falling from racks. The damage state limits were considered as four levels of intensity of loss of containment. Three damage modes (overturning, sliding, and buckling), two types of chemical containers (205 l metal drums and 1000 l IBCs), three types of rack base anchoring (unanchored, anchored-brittle, and anchored-plastic), and four rack heights (3, 4.5, 6, 7.5, 9 m) were considered in the analysis. Overall, twenty-four fragility curves were developed based on twenty-six strong motion records from the PEER Strong Motion database. However, the analytical method employed in this study can also be used for deriving fragility curves for other merchandise types of racking structures. In order to assess the natech risk of a chemical rack containing a flammable substance, to test the developed fragility curves, and to illustrate the natech risk assessment and mapping capabilities of RAPID-N, a case study based on the 1786 Olivieri earthquake scenario was conducted. The findings demonstrate that chemical racks loaded with IBCs are more vulnerable than those loaded with drums. Moreover, although a very robust anchorage reduces the probability of collapse of the rack, it increases the probability of chemical containers falling.