Defects associated with dimensional and geometric variations (tolerance issues) are amongst the most costly and recurring defects in construction projects, yet the identification and mitigation of the causes of tolerance issues appear to be lacking in the construction industry. To enable the development of widely acceptable solutions for the perennial challenge of tolerance management, a more in-depth understanding of causes of tolerance issues should be established. The aim of the research presented in this paper is to identify the potential causes of tolerance issues in construction based on a literature review and empirical studies. This research uses a case study approach. The empirical data is collected through direct observations, group interviews, semi-structured interviews and document reviews. Having triangulated the findings, a list of eighteen potential causes were derived for the eleven observed tolerance issues in two case study projects. The contribution of this paper to knowledge in engineering management is fourfold: (1) the limitations of prior studies on causes of tolerance issues are revealed, (2) the empirical studies led to not only verifying and refining the causes collected from the literature by considering them in the context of the identified tolerance issues, but also finding new causes in the context of tolerance management when compared to literature, (3) the identified causes provide insight into reasons behind the recurrence of tolerance issues across the industry, and (4) it investigates the causes of tolerance issues while balancing managerial and engineering views. The findings of this study provide a pivotal basis for construction practitioners to develop effective solutions for tolerance management whereby tolerance risks can be identified and mitigated in a prescient manner, which can result in a significant amount of savings.