The evaluation of systematic desensitization to treat separation-related problem behaviours, such as destruction of property, excessive barking, or house-soiling, has tended to rely on single case-studies. Eight dogs exhibiting separation-related behaviour, and their owners, participated in a controlled experiment using a within-subjects design to evaluate the efficacy of a combination of systematic desensitization and counter-conditioning. Treatment produced significant reductions in both the frequency (T(9)) = 0.0, P = 0.008) and the severity (T(9)) = 0.0, P = 0.008) of separation-related behaviours compared to baseline. Six dogs, for which follow-up data were obtained three months after treatment ended, showed almost complete elimination of the problem behaviour. The use of counter-conditioning, and other behavioural advice, did not appear to be related to the success of the treatment, suggesting that systematic desensitization was the critical element. Speed of progress and final success was not related to the consistency with which the owners applied systematic desensitization, indicating that even when owners apply systematic desensitization haphazardly, it can still be successful in treating separation-related behaviour in dogs.