We used new methods to examine differences in population-based cancer survival between six prefectures in Japan, after adjustment for age and stage at diagnosis. We applied regression models for relative survival to data from population-based cancer registries covering each prefecture for patients diagnosed with stomach, lung, or breast cancer during 1993-1996. Funnel plots were used to display the excess hazard ratio (EHR) for each prefecture, defined as the excess hazard of death from each cancer within 5 years of diagnosis relative to the mean excess hazard (in excess of national background mortality by age and sex) in all six prefectures combined. The contribution of age and stage to the EHR in each prefecture was assessed from differences in deviance-based R(2) between the various models. No significant differences were seen between prefectures in 5-year survival from breast cancer. For cancers of the stomach and lung, EHR in Osaka prefecture were above the upper 95% control limits. For stomach cancer, the age- and stage-adjusted EHR in Osaka were 1.29 for men and 1.43 for women, compared with Fukui and Yamagata. Differences in the stage at diagnosis of stomach cancer appeared to explain most of this excess hazard (61.3% for men, 56.8% for women), whereas differences in age at diagnosis explained very little (0.8%, 1.3%). This approach offers the potential to quantify the impact of differences in stage at diagnosis on time trends and regional differences in cancer survival. It underlines the utility of population-based cancer registries for improving cancer control.