The goals of clinical trials designed to establish claims for equivalency or superiority of treatment for periodontitis must be clearly stated and defined in terms of measurable and meaningful response variables. It is suggested that these clinical trials use designs that compare new treatment methods to basic periodontal therapy which consists of thorough scaling and root planing, oral hygiene instruction, and regular maintenance care. The primary response variable should be clinical attachment level. It is important to document changes in probing depth since this is a meaningful measure to many clinicians. Gingival inflammation and bleeding should be used as secondary response variables because these are not necessarily indicative of progressive periodontal destruction. Radiographic measures of disease may be useful as primary response variables if safe, reproducible and valid methods of measuring change are utilized. Microbiological monitoring should be a secondary response variable because of numerous questions concerning sampling methodology, quantitative expression of data, and meaningful interpretation in terms of relevance to disease activity. The length of periodontitis trials should be set at a minimum of 9 months if claims of superiority or equivalency are made compared to basic periodontal therapy. Calibration trials should be included and measurement error should be expressed in terms that are meaningful to the clinician while retaining statistical validity. Statistical methods for determining change should take into account site and subject heterogeneity, bursts of change and gradual change over time. It is important that statistical techniques be used that detect change as early as possible and that appropriate consideration be given to the clinical implications of the type, magnitude and duration of change in outcome variables.