diff --git a/include/method_enums.hpp b/include/detect_breakends/method_enums.hpp
similarity index 100%
rename from include/method_enums.hpp
rename to include/detect_breakends/method_enums.hpp
diff --git a/include/detect_breakends/aligned_segment.hpp b/include/structures/aligned_segment.hpp
similarity index 100%
rename from include/detect_breakends/aligned_segment.hpp
rename to include/structures/aligned_segment.hpp
diff --git a/include/breakend.hpp b/include/structures/breakend.hpp
similarity index 100%
rename from include/breakend.hpp
rename to include/structures/breakend.hpp
diff --git a/include/cluster.hpp b/include/structures/cluster.hpp
similarity index 100%
rename from include/cluster.hpp
rename to include/structures/cluster.hpp
diff --git a/include/junction.hpp b/include/structures/junction.hpp
similarity index 100%
rename from include/junction.hpp
rename to include/structures/junction.hpp
diff --git a/src/detect_breakends/junction_detection.cpp b/src/detect_breakends/junction_detection.cpp
index 874b1c64..80dcad1c 100644
--- a/src/detect_breakends/junction_detection.cpp
+++ b/src/detect_breakends/junction_detection.cpp
@@ -4,10 +4,10 @@
 #include <seqan3/io/alignment_file/input.hpp>   // SAM/BAM support
 #include <seqan3/io/sequence_file/output.hpp>   // FASTA support
 
-#include "cluster.hpp"                          // for class Cluster
-#include "detect_breakends/aligned_segment.hpp" // for struct AlignedSegment
 #include "detect_breakends/bam_functions.hpp"   // for hasFlag* functions
-#include "junction.hpp"                         // for class Jnction
+#include "structures/aligned_segment.hpp"       // for struct AlignedSegment
+#include "structures/cluster.hpp"               // for class Cluster
+#include "structures/junction.hpp"              // for class Junction
 
 using seqan3::operator""_cigar_op;
 using seqan3::operator""_tag;
diff --git a/src/find_deletions/deletion_finding_and_printing.cpp b/src/find_deletions/deletion_finding_and_printing.cpp
index 5e3aa3ac..8c78d644 100644
--- a/src/find_deletions/deletion_finding_and_printing.cpp
+++ b/src/find_deletions/deletion_finding_and_printing.cpp
@@ -2,7 +2,7 @@
 
 #include <iostream> // for std::cout
 
-#include "junction.hpp"                         // for class Junction
+#include "structures/junction.hpp"              // for class Junction
 #include "variant_parser/variant_record.hpp"    // for class variant_header
 
 /*! \brief Reads the input junction file and stores the junctions in a vector.