Across low- and middle-income countries on the one hand, and high-income countries on the other, there is confusion in the terminology relating to the study of health services and health systems. This commentary discusses health policy and systems research (HPSR) methods, drawing on the health services research literature and on recent work on HPSR. An earlier version of the text was written to contribute to discussions at a meeting organized by the Alliance for Health Policy and Systems Research, an agency set up in 1998 to promote and support such research in low- and middle-income countries. The paper comments on the field of HPSR methods, suggests priorities and identifies challenges facing the field of HPSR.