Conceptually, clinical guidelines and professional autonomy have a paradoxical relationship. Despite being the quintessence of medical knowledge at the corporate level, guidelines diminish the clinical autonomy of individual practitioners, and therefore threaten medicine's justification for its autonomy. Theorists have argued that professional autonomy will be retained through elite dominance of practitioners, while comparative research suggests that economic autonomy can be traded off to retain clinical autonomy. Under government pressure to regulate the growth of Ontario physicians' fee-for-service public expenditure, the profession's representative organization, the Ontario Medical Association (OMA), promoted voluntary clinical guidelines, hoping to both constrain costs and preserve professional control over the content of medical care. The OMA collaborated with the Ministry of Health in developing guidelines and establishing a provincial centre for health service research. Ontario's practitioners disregarded the OMA's exhortations to implement clinical guidelines, suggesting that in the absence of external constraints, practitioners can subvert elite dominance. However, practitioners' unchecked clinical and economic autonomy, combined with evidence of wide provincial variations in medical care, served to legitimize the government's increasingly unilateral control over the schedule of insured medical services, and, in 1993, their imposition of a global cap on physicians' fee-for-service income pool. When analysed in the context of ongoing Ministry-OMA relations, the failure of the OMA's guidelines strategy to constrain medical service costs has expedited an overall decline in medical autonomy in Ontario. The emergence and course of Ontario's clinical guidelines movement is consistent with the view that medical autonomy is contingent upon broad class forces, and the conceptualization of professional organizations as instruments for mediated occupational control.