■ Does the charity practice “joint cost allocation?”

This is accounting jargon for lumping in fund-raising or solicitation with the charity’s program expenses. According to the BBB Wise Giving Alliance, more than 20 percent of nationally solicited charities it reviews employ this practice, which could muddy the waters in gauging how much is really being spent on the charity’s mission. To get a clearer picture, you will need to identify the charity’s primary purpose. If it is mainly a grass-roots lobbying or public awareness organization (which means you may not be able to deduct your donation), then joint cost allocation may make sense. If it devotes its efforts to financing research, then the allocation may be a red flag.

■ How does the charity evaluate its effectiveness?

You should be able to see some examples in its annual reports. Also, ask the charity directly about its successes. Does the organization use independent auditors to benchmark its performance? Where has it failed? A transparent charity should provide this information along with progress reports.

Eric Friedman, author of “Reinventing Philanthropy” (Potomac Books, 2013), says charities that cannot gauge their effectiveness through benchmarks “may have effective programs, but it’s hard for donors to understand how effective or compare them to other options. I’ve stopped focusing on financial measures, which can be misleading.”

■ Is the mission supported by academic research?

Organizations may be funding ineffective ways of addressing their mission. A boutique charity information service like GiveWell recommends only three organizations a year out of the hundreds it has considered since its founding in 2007. GiveWell performs extensive research to show that recommended charities are “proven, cost-effective, scalable and transparent,” said Alexander Berger, its senior research analyst. “Because we’re aiming to find the best giving opportunities possible — not to rate every charity — we don’t research charities that are unlikely to excel on our criteria.”

■ Watch out for red flags.

Because nonprofit accounting and reporting can be incomplete, suspicious activity can be hidden. Daniel Borochoff, president of CharityWatch, formerly known as the American Institute of Philanthropy, rates 600 charities with a grading system from A to F — and takes a watchdog approach that tries to expose nonprofit abuses. “There’s a lot of sneaky reporting going on,” Mr. Borochoff said. He said chicanery could often be found in “gifts in kind,” where donations may be overvalued, or in organizations with emotional appeals — some charities involving animals, children, first responders and veterans. They may be little more than aggressive fund-raising operations that do little for their missions, or funds that are diverted to officers or other purposes.

■ Do you need comprehensive advice?

If you are also concerned about tax or estate planning considerations, it would make sense to work with a wealth manager, estate-planning lawyer or certified financial planner. Many advisers also have insights into nonprofit accounting that can help you vet a charity on a deeper level. Robert J. DiQuollo, chief executive of Brinton Eaton Wealth Advisors in Madison, N.J., said he could scrutinize nonprofit line items like executive salaries and program-related expenses. “We always approach the charity directly,” Mr. DiQuollo said, “to make sure that the charity is spending money on what the donor wants.”

■ Is the charity sitting on too much cash?

You need to know if the charity is putting its cash to good use or reserving it for some other purpose. According to Wise Giving Alliance standards, “the charity’s unrestricted net assets available for use should not be more than three times the size of the past year’s expenses or three times the size of the current year’s budget, whichever is higher.” This is something you may need an experienced accountant to evaluate. The bottom line: As a donor, you need to know if your money will be put to work immediately or sidelined.