Juvenile idiopathic arthritis (JIA) is the most common paediatric rheumatic condition but still a disease of low prevalence. The paediatric rheumatology research community is often faced with significant challenges if only the common study designs such as the parallel group randomised control design are used. This systematic review evaluates the clinical designs used to date in experimental studies of JIA. Our review discusses the concept, advantages and disadvantages of each trial design type. Innovative trial designs are one of the ways we will move forward in developing an evidence base for paediatric rheumatology practice.