Objective: The aim of the present study was to examine selection in a general practice-based pregnancy cohort. Design: Survey linked to administrative register data. Setting and subjects: In spring 2015, GPs were recruited from two Danish regions. They were asked to invite all pregnant women in their practice who had their first prenatal care visit before 15 August 2016 to participate in the survey. Outcome measures: The characteristics of GPs and the pregnant women were compared at each step in the recruitment process–the GP’s invitation, their agreement to participate, actual GP participation, and the women’s participation–with an uncertainty coefficient to quantify the step where the largest selection occurs. Results: Significant differences were found between participating and non-participating practices with regards to practice characteristics such as the number of patients registered with the practice, the age and sex of doctors, and the type of practice. Despite these differences, the characteristics of the eligible patients differed little between participating and non-participating practices. In participating practices significant differences were, however, observed between recruited and non-recruited patients. Conclusion: The skewed selection of patients was mainly caused by a high number of non-participants within practices that actively took part in the study. We recommend that a focus on the sampling within participating practices be the most important factor in representative sampling of patient populations in general practice.Key points Selection among general practitioners (GPs) is often unavoidable in practice-based studies, and we found significant differences between participating and non-participating practices. These include practice characteristics such as the number of GPs, the number of patients registered with the GP practice, as well as the sex and age of the GPs. •Despite this, only small differences in the characteristics of the eligible patients were observed between participating and non-participating practices. •In participating practices, however, significant differences were observed between recruited and non-recruited patients. •Comprehensive sampling within participating practices may be the best way to generate representative samples of patients.