Existing methods for setting confidence intervals for the difference θ between binomial proportions based on paired data perform inadequately. The asymptotic method can produce limits outside the range of validity. The ‘exact’ conditional method can yield an interval which is effectively only one‐sided. Both these methods also have poor coverage properties. Better methods are described, based on the profile likelihood obtained by conditionally maximizing the proportion of discordant pairs. A refinement (methods 5 and 6) which aligns 1−α with an aggregate of tail areas produces appropriate coverage properties. A computationally simpler method based on the score interval for the single proportion also performs well (method 10). © 1998 John Wiley & Sons, Ltd.