Context: Removal of wastes is a crucial area in lean software development. It has been found that there was little evidence on root causes of wastes in lean software development. Root causes from the state of practice had not being investigated. Furthermore, relations between wastes were now successfully exposed through root cause identifications process. Objectives: The objective of this study was to perform an in-depth investigation to identify causes which lead to wastes in Lean software development process in the context of medium to large software development. To this end, researcher also identified relationships that exist between wastes. Methods: The researcher conducted Literature review to look for evidence on waste related activities offered in peer-reviewed literature. Furthermore, the author conducted seven semi-structured interviews and used Grounded Theory method for both literature and interview data analysis. Results: The researcher identified three categories of factors of wastes. Namely, Technical, Non-technical and Global software product development. In the technical category, factors relating to different technical aspects to build a product such as required resource issues, solving complexity issues among others were identified. Similarly, factors relating to people knowledge, management issues as well as factors that bothered on communication, coordination and temporal distance were identified as non-technical and global software product development respectively. For all seven kinds of wastes the root causes were identified.