Internet based cognitive behavioural therapy (CBT) is efficacious for the treatment of anxiety and depression. The current study aimed to examine the effectiveness of internet based CBT prescribed by primary care clinicians for the treatment of depression and generalised anxiety disorder. Psychological distress data from 302 patients who completed an online CBT course for depression and 361 patients who completed an online CBT course for generalised anxiety disorder were subjected to growth mixture analysis. For both disorders psychological distress decreased across each lesson in a quadratic trend. Two classes of individuals were identified with different trajectories of change: a large group of individuals who responded well to the courses and a smaller group of individuals with a lower response. Both groups were similar with respect to sociodemographic characteristics however the low responders tended to have higher levels of symptom severity and psychological distress at baseline in comparison to the responders. For the majority of patients (75-80%) the internet CBT courses for depression and generalised anxiety disorder were effective. Further research is required to identify and effectively treat the smaller proportion of patients who did not improve during internet CBT.