Objectives Despite the long-term use and evidence-based efficacy of meditation and mindfulness-based interventions, there is still a lack of data about the possible unwanted effects (UEs) of these practices. The aim of this study was to evaluate the occurrence of UEs among meditation practitioners, considering moderating factors such as the type, frequency, and lifetime duration of the meditation practices. Methods An online survey was developed and disseminated through several websites, such as Spanish-, English- and Portuguese-language scientific research portals related to mindfulness and meditation. After excluding people who did not answer the survey correctly or completely and those who had less than two months of meditation experience, a total of 342 people participated in the study. However, only 87 reported information about UEs. Results The majority of the practitioners were women from Spain who were married and had a University education level. Practices were more frequently informal, performed on a daily basis, and followed by focused attention (FA). Among the participants, 25.4% reported UEs, showing that severity varies considerably. The information requested indicated that most of the UEs were transitory and did not lead to discontinuing meditation practice or the need for medical assistance. They were more frequently reported in relation to individual practice, during focused attention meditation, and when practising for more than 20 minutes and alone. The practice of body awareness was associated with UEs to a lesser extent, whereas focused attention was associated more with UEs. Conclusions This is the first large-scale, multi-cultural study on the UEs of meditation. Despite its limitations, this study suggests that UEs are prevalent and transitory and should be further studied. We recommend the use of standardized questionnaires to assess the UEs of meditation practices.