Patient-based substudies from BEACH: abstracts and research tools 1999-2006 is the 20th report in the general practice series produced by the Australian General Practice Statistics and Classification Centre, University of Sydney, a collaborating unit of the Australian Institute of Health and Welfare. This report includes abstracts for, and research tools used, in 104 general practice substudies conducted as part of the BEACH (Bettering the Evaluation and Care of Health) program. BEACH is a continuous national study of general practice activity. Since 1998 over 9,000 GPs have recorded details regarding approximately 900,000 GP-patient encounters on structured paper forms. The substudies are referred to as SAND (Supplementary Analysis of Nominated data). There is a SAND section at the bottom of every encounter form, in which we investigate aspects of patient health or health care delivery not covered by the encounter-based data. We hope that this report will assist GPs and other researchers by providing them with a wide range of tools that have demonstrated acceptability and utility, that are useable in the confines of general practice patient consultations, and which have already been approved by recognised ethics committees.