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Past research has demonstrated that the explicit use of protected attributes in machine learning can improve both performance and fairness. Many machine learning algorithms, however, cannot directly process categorical attributes, such as country of birth or ethnicity. Because protected attributes frequently are categorical, they must be encoded as features that can be input to a chosen machine learning algorithm, e.g.\ support vector machines, gradient boosting decision trees or linear models. Thereby, encoding methods influence how and what the machine learning algorithm will learn, affecting model performance and fairness. This work compares the accuracy and fairness implications of the two most well-known encoding methods: \emph{one-hot encoding} and \emph{target encoding}. We distinguish between two types of induced bias that may arise from these encoding methods and may lead to unfair models. The first type, \textit{irreducible bias}, is due to direct group category discrimination, and the second type, \textit{reducible bias}, is due to the large variance in statistically underrepresented groups. We investigate the interaction between categorical encodings and target encoding regularization methods that reduce unfairness. Furthermore, we consider the problem of intersectional unfairness that may arise when machine learning best practices improve performance measures by encoding several categorical attributes into a high-cardinality feature.