To estimate prevalence of chronic conditions among patients seeing a general practitioner (GP), patients attending general practice at least once in a year, and the Australian population. A sub-study of the BEACH (Bettering the Evaluation and Care of Health) program, a continuous national study of general practice activity conducted between July 2008 and May 2009. Each of 290 GPs provided data for about 30 consecutive patients (total 8,707) indicating diagnosed chronic conditions, using their knowledge of the patient, patient self-report, and patient's health record. Estimates of prevalence of chronic conditions among patients surveyed, adjusted prevalence in patients who attended general practice at least once that year, and national population prevalence. Two-thirds (66.3%) of patients surveyed had at least one chronic condition: most prevalent being hypertension (26.6%), hyperlipidaemia (18.5%), osteoarthritis (17.8%), depression (13.7%), gastro-oesophageal reflux disease (11.6%), asthma (9.5%) and Type 2 diabetes (8.3%). For patients who attended general practice at least once, we estimated 58.8% had at least one chronic condition. After further adjustment we estimated 50.8% of the Australian population had at least one chronic condition: hypertension (17.4%), hyperlipidaemia (12.7%), osteoarthritis (11.1%), depression (10.5%) and asthma (8.0%) being most prevalent. This study used GPs to gather information from their knowledge, the patient, and health records, to provide prevalence estimates that overcome weaknesses of studies using patient self-report or health record audit alone. Our results facilitate examination of primary care resource use in management of chronic conditions and measurement of prevalence of multimorbidity in Australia.