The objective of the study was to determine the long-term functional outcome of chronic spondylarthropathy (SpA) when measured by various functional indices. This information is important in the planning of long-term intervention studies and selection of the best follow-up methods. The study group consisted of 65 patients (21 women and 44 men) with SpA. Their mean age was 49 years and the mean age from diagnosis was 12 years. They completed several questionnaires (developed for the evaluation of functional capacity or the state of health of patients with SpA) at the beginning of the study and 3 years later. The questionnaires were: the Bath Ankylosing Spondylitis Functional Index (BASFI), the Dougados Functional Index (DFI), the Health Assessment Questionnaire for Spondylarthropathies (HAQ-S), the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), the Bath Ankylosing Spondylitis Patient Global Assessment (BAS-G) and Stiffness-VAS (on a visual analogue scale). We also asked the patients to inform us if something had occurred in their lives during the follow-up that might have affected their health. Most of the indices (BASFI, DFI, BASDAI, BAS-G and Stiffness-VAS, but not HAQ-S) showed a statistically significant reduction in the functional capacity or state of health of the patients during the follow-up. Many factors occurring during the 3-year period may have influenced the results of the indices. The natural course of the functional capacity of patients with SpA appears to be one of impairment, when evaluated using these indices. Our experience also showed that it is very difficult to separate any effect of a single treatment intervention (e.g. rehabilitation) in a long-term follow-up study, as so many interfering factors, e.g. life events and health-related factors, may affect the follow-up population over several years.