Tourette Syndrome (TS) is a neurodevelopmental disorder that starts in childhood. It is marked by multiple motor and vocal tics and a fluctuating course with recurrent time periods of symptom exacerbation followed by symptom remission. TS is considered a disorder of complex etiology that involves the interaction of multiple genetic and environmental factors. Previous studies have implicated regulation of the immune system in TS patients, although this remains a matter of debate. Here we present a genome-wide gene expression study comparing data from TS patients at time points of symptom exacerbation and remission as well as upon symptom onset for newly diagnosed patients, with differentially gene expression analysis, co-expression analysis and pathway analysis. Although the fold change of each regulated gene was very mild, it is the first time that changes in the regulation of the immune system have been implicated at different time points in TS patients.