The aim of this study was to identify barriers to effective breast, cervical and colorectal cancer screening programmes throughout the whole of the European region using the Barriers to Effective Screening Tool (BEST). The study was part of the scope of the EU-TOPIA (TOwards imProved screening for breast, cervical and colorectal cancer In All of Europe) project and respondents were European screening organisers, researchers and policymakers taking part in a workshop for the project in Budapest in September 2017. 67 respondents from 31 countries responded to the online survey. The study found that there are many barriers to effective screening throughout the system from identification of the eligible population to ensuring appropriate follow-up and treatment for the three cancers. The most common barriers were opportunistic screening, sub-optimal participation, limited capacity (including trained human resource), inadequate and/or disjointed information technology systems and complex administration procedures. Many of the barriers were reported consistently across different countries. This study identified the barriers that, in general, require further investment of resources.