Background Changes in the epidemiologic and clinical features of measles have resulted in diagnostic difficulties in distinguishing between measles and other rash and fever illnesses such as rubella. The objectives of this article are to report the true morbidity and epidemiologic and clinical features of measles and rubella, provide objective diagnostic indicators for distinguishing between the 2 diseases, and provide a time-efficient scientific basis for accurately evaluating the effectiveness of immunization with the measles vaccine and regulating the control strategies for measles in the rural areas of China in the cold chain era. Methods From 1992 to 2002, patients with measles and rubella were recorded and reported routinely in the rural disease surveillance spots of Jingzhou District, Hubei Province, by collecting their sera and testing for measles and rubella IgM and IgG antibodies. Results Over the 11-year study period, 146 cases of measles were reported in the disease surveillance spots. The annual incidence of measles was highest in 1999 (118.8/100,000 population). The incidence of measles in the 4–6 and 7–15 year old age groups were higher than in other age groups. During 5 outbreaks of measles, a total of 128 cases were reported, accounting for 87.7% of the total number of measles cases. A total of 566 rubella cases were reported, with 3 epidemic peaks (in 1992, 1997 and 2002). The incidence of rubella in the 4–6 and 7–15 year old age groups were higher than in other age groups. There were 13 outbreaks of rubella, with 547 cases being reported, accounting for 96.6% of the total number of rubella cases. Accuracy of the clinical diagnosis of measles was 40%, while it was 100% for rubella. The proportions of patients who had a moderate to high fever (= 38.6°C) in the measles group (89.5%) and the combined infection (both measles and rubella) group (90%) were significantly higher than that of the rubella group (30.6%). The proportions of patients whose prodromal stage lasted = 3 days in the former 2 groups (68.4% and 95%, respectively) were significantly higher than that of the rubella group (16.7%). The proportions of patients whose exanthema lasted = 4 days in the former 2 groups (78.9% and 75%, respectively) were significantly higher than that of the rubella group (26.9%). Conclusion Measles and rubella are 2 common communicable diseases in the children of Jingzhou District, with outbreaks being the main epidemic form. Some clinical features such as temperature, duration of the prodromal stage and exanthema are different in measles and rubella, and they can be useful in distinguishing between the 2 diseases. Accuracy in the clinical diagnosis of measles should be improved by enhancing serologic testing for measles and rubella, and by identifying patients' specific clinical characteristics.