The current study describes a system-wide method of evaluating detection strategies for co-occurring disorders within a state mental health system. Information technology was used to merge administrative datasets from the New Jersey mental health and substance abuse systems and identify individuals treated in both systems. We measured a 53% detection rate of substance use disorders amongst adult patients in the mental health system with particularly low detection rates in acute settings (49.0%) and among female (43.7%), older (36.2%), and psychotic patients (43.6%). The methodology described here could help evaluate critical aspects of ongoing state co-occurring disorder quality improvement initiatives.