Most organizations use per diems as a way to reimburse out-of-pocket expenses for travel and to encourage staff to attend professional development activities. However, weaknesses in policy design and control of spending can cause problems, including distortions of human resource systems, fraud and abuse by staff. Governments and non-governmental organizations need to adopt and implement fair, transparent, and efficient policies which provide adequate compensation for work-related travel without creating adverse incentives. This toolkit proposes a methodology to study per diem policies of the health sector in a given country, in government, international, or non-governmental organizations. It presents tools designed to describe and analyse the different types of per diems, policy characteristics and control systems, per diem spending, and attitudes and perceptions of staff as a means for identifying corruption risks. The toolkit can also be applied to other sectors with little adaptation.