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The tests uncover sensitive information about banks, such as how many of their loans are likely to go unpaid, but the ECB said there was a strict separation between investors at BlackRock, which owns shares in all top European banks, and the consultancy arm.
The tests are the latest probe of big banks in the euro zone from carmaker Volkswagen's finance arm to France's BNP Paribas.
The ECB, put in charge of monitoring those banks after the financial crash, uses the check to identify problems at lenders.
The consultancy arm of BlackRock, BlackRock Solutions, has experts who help diagnose risks, for example, or put a value on risky loans.
The ECB said there was a separation between the consultancy work and other parts of the parent firm. "Confidentiality of information is secured by the terms of the contract," said a spokesman for the ECB.
BlackRock's consultancy arm has also helped the ECB design a scheme to buy asset-backed securities - loans that are bundled together and sold.
The ECB tests will probe 39 banks in the euro zone. The results will be ready toward the middle of the year.