Context: There continues to be concern that research is not addressing the challenges that practice faces. For the benefit of academia and industry, researchers need to be aware of practitioners' challenges and their context so that relevant and applicable research is undertaken. Objective: This paper investigates two research questions: what challenges do agile, practitioners face? and, how do practitioner challenges manifest themselves in an organisational setting? It aims to map the practitioner challenge landscape, explore challenge characteristics, compare findings with previous literature and identify implications for research that is relevant to practice. Method: A combination of methods was used: elicitation of practitioner challenges collected using a Challenge Wall at a series of practitioner events; organisational case study using interviews, document analysis and observation; and online survey. Findings were then compared to previous publications. Results: Challenges collected from the Challenge Wall were grouped under 27 subthemes and seven themes: claims and limitations, organisation, sustainability, culture, teams, scale, and value. Investigating one challenge in the case study uncovered a set of new challenges, which were inter-related. Over 50% of survey respondents experienced challenges highlighted in the case study. Conclusion: The landscape of agile practitioner challenges is complex and intertwined. Some challenges, such as doing agile in a non-agile environment, are multi-dimensional, affect many aspects of practice, and may be experienced simultaneously as business, organisational, social and adaptation problems. Some challenges, such as understanding cultural change or measuring agile value, persist and are hard to address, while others, such as adoption, change focus over time. Some challenges, such as governance and contracts, are under-researched, While others, such as business and IT transformation, have been researched but findings" have not had the expected impact. Researchers wishing to address practitioner challenges need to treat them in context rather than in isolation and improve knowledge transfer. (C) 2016 Elsevier B.V. All rights reserved.