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Because low quality code can cause serious problems in software systems, students learning to program should pay attention to code quality early. Although many studies have investigated mistakes that students make during programming, we do not know much about the quality of their code. This study examines the presence of quality issues related to program flow, choice of programming constructs and functions, clarity of expressions, decomposition and modularization in a large set of student Java programs. We investigated which issues occur most frequently, if students are able to solve these issues over time and if the use of code analysis tools has an effect on issue occurrence. We found that students hardly fix issues, in particular issues related to modularization, and that the use of tooling does not have much effect on the occurrence of issues.