WHAT DID WE DO?: As the amount of alternative funding for physician services grows in Canada, the usefulness of fee-for-services (FFS) payment data as a source of population-based information declines. This paper describes methods used to develop and validate an anonymous registry of the physician workforce to support policy-relevant analyses in environments where doctors are increasingly funded through diverse arrangements. WHAT DID WE LEARN?: Among the 8,558 physicians in clinical practice in British Columbia in 2004, 97% could be identified via FFS payment data. In 1996, 2000 and 2004, a similar number of physicians in clinical practice (N=340, 326, 290) did not submit FFS claims, and a stable proportion of these doctors (65%, 67%, 69%) could be identified using hospital discharge abstract data. Province-wide, local health areas varied in the proportion of total physicians' expenditures in 2004 attributable to FFS payments (0 to 100%). WHAT ARE THE IMPLICATIONS?: FFS and hospital files could be used in tandem to identify physicians in clinical practice in order to create complete registries intended to support population-based workforce analyses. FFS and alternative funding payment files could be used together to calculate each physician's income and clinical activity, and to identify physicians for whom there is high likelihood of measurement error because they reside in local health areas where a large proportion of clinical activity is not captured. RECOMMENDATIONS: Systems designed to track alternative funding should be uniformly structured within and across jurisdictions to maintain or increase the availability of population-based clinical data useful for secondary analyses. Only then can these data be used to support Canadian policy, management and clinical decision-making.