This paper is the second in a four-part series outlining treatment planning at periodontal reassessment. The first article focussed on the information that should be gathered at the reassessment appointment. Treatment can involve a range of non-surgical and surgical approaches. A variety of general, practical and local site factors can affect the choice of one option over another in choosing the most predictable treatment option. Residual periodontal probing depths can be associated with both systemic and local factors. This article (part 2) outlines systemic factors that need to be assessed when faced with residual periodontal probing depths.