Clinician-guided Internet-based cognitive behavioural therapy (iCBT) programs are clinically effective at treating specific anxiety disorders. The present study examined the efficacy of a transdiagnostic Internet-based cognitive behavioural treatment (iCBT) program to treat more than one anxiety disorder within the same program (the Anxiety Program). Eighty six individuals meeting diagnostic criteria for generalized anxiety disorder (GAD), panic disorder, and/or social phobia were randomly assigned to a treatment group, or to a waitlist control group. Treatment consisted of CBT based online educational lessons and homework assignments, weekly email or telephone contact from a clinical psychologist, access to a moderated online discussion forum, and automated emails. An intention-to-treat model using the baseline-observation-carried-forward principle was employed for data analyses. Seventy-five percent of treatment group participants completed all 6 lessons within the 8 week program. Post-treatment data was collected from 38/40 treatment group and 38/38 control group participants, and 3-month follow-up data was collected from 32/40 treatment group participants. Relative to controls, treatment group participants reported significantly reduced symptoms of anxiety as measured by the Generalized Anxiety Disorder - 7 Item, Social Phobia Screening Questionnaire, and the Panic Disorder Severity Rating Scale - Self Report Scale, but not on the Penn State Worry Questionnaire, with corresponding between-groups effect sizes (Cohen's d) at post-treatment of 0.78, 0.43, 0.43, and 0.20, respectively. The clinician spent a total mean time of 46 min per person over the program, participants rated the procedure as moderately acceptable, and gains were sustained at follow-up. Modifications to the Anxiety program, based on post-treatment feedback from treatment group participants, were associated with improved outcomes in the control group. These results indicate that transdiagnostic programs for anxiety disorders may be successfully administered via the Internet.