The C preprocessor cpp is a powerful and language-independent tool, widely used to implement variable software in different programming languages (C, C++) using conditional compilation. Preprocessor annotations can used on different levels of granularity such as functions or statements. In this paper, we investigate whether there is a relation between code clones and preprocessor annotations. Specifically, we address the question whether the discipline of annotation has an effect on code clones. To this end, we perform a case study on fifteen different C programs and analyze them regarding code clones and #ifdef occurrences. We found only minor effects of annotations on code clones but a relationship between annotations that align with the code structure (and code clones). With this work, we provide new insights why code clones occur in C programs. Furthermore, the results can support the decision whether it is beneficial to remove clones or not.