The number of trade disputes between Thailand and Australia is small. Rarely are they lodged as formal disputes" rather they are the subject of bilateral discussions. The disputes tend to be about Thai food exports and are related to sanitary and phytosanitary measures imposed by Australia. Australia over many years has developed a very tight quarantine regime. This is no doubt largely due to the fact that Australia, as an island nation, has natural protection from imported diseases. As international trade has increased Australia's trading partners, have become concerned that Australia's quarantine regime lacks transparency and is based on prohibition rather than risk. Thailand has been one of those concerned trading partners. This paper looks at two particular cases. The first is a case brought in the WTO by the European Union against Australia" Thailand reserved its third-party rights in this case. The terms of the agreement between Australia and the European Commission clearly led to a much more rigorous risk based assessment by Australia in relation to SPS Agreement matters. In the second case related to prawns/shrimps, Australia issued its preliminary risk assessment which was challenged by a number of developing countries who presented their case to Australian authorities. The outcome was a more transparent process with an acceptable risk level based on scientific principles.