Nonprofit organizations do not issue shares and their missions are not to maximize profit. While nonprofit managers are not accountable to shareholders, they are accountable to donors and grantors who provide an important source of capital. These donors and grantors do not have limitless resources and, therefore, nonprofit organizations must compete for funding. If an organization has an internal control problem, donors and grantors could choose to support another organization where, presumably, the capital is used more efficiently. The main purpose of this study is to explore warning signs of existence internal control problems in nonprofit organizations. The final sample used for this study consists of 162 members of Iranian Association of Certified Public Accountants. Also, data were collected using a questionnaire survey. Descriptive statistics and Friedman test were used to analyze data. The result of this study showed that from viewpoint of the members of Iranian Association of Certified Public Accountants, organizational complexity, deficit, new grantee, going concern risk, risk level and smallness of audit firm in prior year are important warning signs of existence internal control problems in nonprofit organizations.