The following information is summarized from these sources: Independent Sector; Guidestar
In August 2006, the US Congress passed and President Bush signed pension reform legislation that included a package of charitable incentives and safeguards. The law (H.R. 4)contains giving incentives, an IRA rollover provision, and a series of safeguards designed to prevent people from using nonprofit organizations for personal benefit and the ensure donations are used for charitable purposes.
The IRA rollover allows people age 70.5 and older to make charitable donations up to $100,000 from an IRA without counting the donation as taxable income. The law does not include a charitable deduction for taxpayers who don’t itemize deductions, as had been supported by many nonprofit groups. The law no longer requires that nonprofits have their UBIT (Unrelated Business Income Tax) liability certified by an outside party. It still corrects the treatment of payments by affiliated organizations, but now only requires that nonprofits make their Form 990-T public, excluding information that would jeopardize the operations of unrelated business activities.
The IRS is one of the few federal agencies who had received additional funding. They now have more staff to support the enforcement in the tax-exempt sector as one of their top 4 priorities. In 2004 they began targeting credit counseling services for review and examination. Many of their audits resulted in a withdrawal of the organization’s tax-exempt status. This was often due to a lack of public benefit, i.e. education and counseling relative to credit issues.
Also, the IRS released a report earlier in 2006 on political activity by 501(c)(3) organizations. It found that "nearly three-quarters of the organizations examined under this initiative had engaged in prohibited political activities." This included supporting/opposing candidates, posting campaign signs, and allowing certain candidates to speak at their functions. The IRS issued a report on political activity in early 2007- see http://www.irs.gov/charities/article/0,,id=154622,00.html
Another major area of interest is executive compensation. Compliance checks by the IRS are keyed to the IRS Form 990 and include questions about sales, exchanges, or leasing of property which may trigger conflict of interest issues and questions about improper private benefit.