Cost-effectiveness analysis (CEA) compares the costs and outcomes of two or more technologies. However, there is no consensus about which measure of effectiveness should be used in each analysis. Clinical researchers have to select an appropriate outcome for their purpose, and this choice can have dramatic consequences on the conclusions of their analysis. In this paper we present a Bayesian cost-effectiveness framework to carry out CEA when more than one measure is considered. In particular, we analyse the case in which two measures of effectiveness, one binary and the other continuous, are considered. Decision-making measures, such as the incremental cost-effectiveness ratio, incremental net-benefit and cost-effectiveness acceptability curves, are used to compare costs and one measure of outcome. We propose an extension of cost-acceptability curves, namely the cost-effectiveness acceptability plane, as a suitable measure for decision taking. The models were validated using data from two clinical trials. In the first one, we compared four highly active antiretroviral treatments applied to asymptomatic HIV patients. As measures of effectiveness, we considered the percentage of patients with undetectable levels of viral load, and changes in quality of life, measured according to EuroQol. In the second clinical trial we compared three methadone maintenance programmes for opioid-addicted patients. In this case, the measures of effectiveness considered were quality of life, according to the Nottingham Health Profile, and adherence to the treatment, measured as the percentage of patients who participated in the whole treatment programme.