BACKGROUND Sickness certification is a routine task of primary care (PC) physicians which has an impact on patients' health, the health care system and the economy. As sickness certification is poorly studied, we quantified sickness certification and explored qualitatively the sickness certification process by Swiss PC physicians. METHODS PC physicians participating in the Swiss Sentinel Surveillance Network (SSSN) recorded the frequency and duration of absence from work of each related consultation and certificate during 2005. Patients' age and gender, reason for sick leave, psychosocial cofactors, problems at the workplace, type of employment, type of occupation, duration of absence (weeks) and type of certificate were registered. Physicians' views on the procedure and their suggestions for change were gathered before and after the study by means of a questionnaire containing four open-ended questions. RESULTS Of the 223 SSSN physicians 73% participated. A total of 24,676 forms issued by 150 physicians were analysed. An average of four certificates was issued per 100 consultations; somewhat fewer by internists than by general practitioners and less in rural areas than urban areas. Psychosocial or work-related factors were mentioned in 20% of the certificates and were more often associated with longer absences from work. These factors were seen as inseparable from the somatic factors. Recommendations for change included the prolongation of self declaration time, a uniform declaration form, availability of an authority to which complex cases can be referred and the use of case management models. CONCLUSIONS Sickness certificates were issued in 4% of GP consultations. This task has been assessed by physicians as part of their function. The certification process should be improved through better coordination and communication between all parties involved: patients, employers, insurers, physicians and politicians.