In the past 10 to 12 years, there have been several statistical issues identified in periodontal research which require and have generated non-standard or new statistical approaches. The purpose of this paper is to give an overview of these issues and approaches. Three general categories of issues are described: (i) statistical methods for detecting when disease progression occurs, and biological theories and corresponding statistical models which attempt to describe how the disease progresses; (ii) design issues in studies of therapeutic efficacy; and (iii) analytic issues arising from periodontal data analysis.