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Clinical trial eligibility criteria define the target patient population for research studies. We assessed the eligibility criteria from 40 different protocols for Type II Diabetes Mellitus and depression (20 protocols each), to determine the extent to which protocol eligibility criteria were similar at three levels (test, test-value, and test-value-time clause). This was done to determine criteria that could be standardized to aid in identification of eligible patients from electronic health records. It was found that Type II Diabetes Mellitus had 36.9% similar and depression protocols had 53.1% similar at the test-value-clause level. This study demonstrates the need for more standardization of study protocol criteria as well as the associated query definitions to be run against the electronic healthcare data. Standardizing criteria based on the similar eligibility criteria between protocols will aid in patient recruitment by being able to reuse criteria and minimizing the time and money it takes to recruit patients.