Aims The standardised mean difference (SMD) is one of the most used effect sizes to indicate the effects of treatments. It indicates the difference between a treatment and comparison group after treatment has ended, in terms of standard deviations. Some meta-analyses, including several highly cited and influential ones, use the pre-post SMD, indicating the difference between baseline and post-test within one (treatment group). Methods In this paper, we argue that these pre-post SMDs should be avoided in meta-analyses and we describe the arguments why pre-post SMDs can result in biased outcomes. Results One important reason why pre-post SMDs should be avoided is that the scores on baseline and post-test are not independent of each other. The value for the correlation should be used in the calculation of the SMD, while this value is typically not known. We used data from an 'individual patient data' meta-analysis of trials comparing cognitive behaviour therapy and anti-depressive medication, to show that this problem can lead to considerable errors in the estimation of the SMDs. Another even more important reason why pre-post SMDs should be avoided in meta-analyses is that they are influenced by natural processes and characteristics of the patients and settings, and these cannot be discerned from the effects of the intervention. Between-group SMDs are much better because they control for such variables and these variables only affect the between group SMD when they are related to the effects of the intervention. Conclusions We conclude that pre-post SMDs should be avoided in meta-analyses as using them probably results in biased outcomes.