Qualitative risk assessment (QRA) can provide decision support in line with the requirement for an objective, unbiased assessment of disease risk according to the Agreement on the Application of Sanitary and Phytosanitary Measures of the World Trade Organization. However, in order for a QRA to be objective and consistently applied it is necessary to standardize the approach as much as possible. This review considers how QRAs have historically been used for the benefit of animal health, what problems have been encountered during their progression, and considers best practice for their future use. Four main elements were identified as having been the subject of some proposed standard methodology: (i) the description of risk levels, (ii) combining probabilities, (iii) accounting for trade volume and time period, and (iv) uncertainty. These elements were addressed in different ways but were highlighted as being fundamental to improving the robustness in estimating the risk and conveying the results to the risk manager with minimal ambiguity. In line with this, several tools have been developed which attempt to use mathematical reasoning to incorporate uncertainty and improve the objectivity of the qualitative framework. This represents an important advance in animal health QRA. Overall, animal health QRAs have established their usefulness by providing a tool for rapid risk estimation which can be used to identify important chains of events and critical control points along risk pathways and inform risk management programmes as to whether or not the risk exceeds a decision-making threshold above which action should be taken. Ensuring a robust objective methodology is used and that the reasons for differences in results, such as assumptions and uncertainty are clearly described to the customer with minimal ambiguity is essential to maintain confidence in the QRA process. However, further work needs to be done to determine if one objective uniform methodology should be developed and considered best practice. To this end, a set of best practice guidelines presenting the optimal way to conduct a QRA and regulated by bodies such as the World Organization for Animal Health or the European Food Safety Authority would be beneficial.