Changes in health according to World Health Organization's International Classification of Functioning, Disability and Health (ICF) after four weeks of pulmonary rehabilitation (PR) were investigated. Gender differences in the response to PR, and the correlation between improvements in the two components of ICF (Body functions and Activities and Participation) were examined. Twenty-two men and 18 women with chronic obstructive pulmonary disease in Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage II-IV attended in-patient, multidisciplinary PR consisting of endurance training four to five times/week at 70% of peak work rate (WRpeak), resistance training three to four times/week at 72% of 15 repetitions maximum, educational sessions and individual counselling. The results were compared to those of 20 Chronic Obstructive Pulmonary Disease (COPD) patients included after the same criteria and investigated while waiting for admission to PR. In the rehabilitation group, we found significant improvements in health related quality of life (HRQoL) (-7 units, St. George's Respiratory Questionnaire), arm (6%) and leg (15%) maximal voluntary contraction, peak oxygen uptake (6%), WRpeak (60%) and treadmill endurance time (93%). At iso-WR, ventilation and dyspnoea were significantly lower, but inspiratory capacity remained unchanged. Improvements in HRQoL correlated with increases in peak ventilation, but not in muscle strength or exercise capacity. Men improved their six-minute walking distance significantly in contrast to women. Clinically important improvements in HRQoL were found in two out of three of the men, and one out of three of the women. Four weeks of intensive PR generated significant health effects comparable to longer lasting programmes. Changes in exercise capacity and muscle strength were not related to improvements in HRQoL. The gender differences in the response to PR deserve attention in future studies.