diff --git a/src/common/counts_header.cpp b/src/common/counts_header.cpp
index 051eb89e..228602fe 100644
--- a/src/common/counts_header.cpp
+++ b/src/common/counts_header.cpp
@@ -18,6 +18,8 @@
 
 #include "counts_header.hpp"
 
+#include <iostream>
+#include <fstream>
 #include <string>
 #include <vector>
 #include <cassert>
@@ -30,6 +32,7 @@
 #include <config.h>
 
 #include "bamxx.hpp"
+#include "dnmt_error.hpp"
 
 using std::vector;
 using std::string;
@@ -52,6 +55,20 @@ write_counts_header_from_chrom_sizes(const vector<string> &chrom_names,
 }
 
 
+void
+write_counts_header_from_file(const string &header_file, bgzf_file &out) {
+  std::ifstream in(header_file);
+  if (!in.is_open()) {
+      throw dnmt_error("failed to open header file: " + header_file);
+  }
+  string line;
+  while(getline(in, line)) {
+    out.write(line + '\n');
+  }
+  in.close();
+}
+
+
 inline bgzf_file &
 getline(bgzf_file &file, kstring_t &line) {
   if (file.f == nullptr) return file;
diff --git a/src/common/counts_header.hpp b/src/common/counts_header.hpp
index bb3f851b..d19d0398 100644
--- a/src/common/counts_header.hpp
+++ b/src/common/counts_header.hpp
@@ -30,6 +30,10 @@ write_counts_header_from_chrom_sizes(const std::vector<std::string> &chrom_names
                                      const std::vector<uint64_t> &chrom_sizes,
                                      bamxx::bgzf_file &out);
 
+void
+write_counts_header_from_file(const std::string &header_file,
+                              bamxx::bgzf_file &out);
+
 // returns -1 on failure, 0 on success
 int
 get_chrom_sizes_for_counts_header(const uint32_t n_threads,
diff --git a/src/utils/xcounts.cpp b/src/utils/xcounts.cpp
index 372f970e..2c77a49a 100644
--- a/src/utils/xcounts.cpp
+++ b/src/utils/xcounts.cpp
@@ -85,6 +85,7 @@ main_xcounts(int argc, const char **argv) {
     bool require_coverage = false;
     size_t n_threads = 1;
     string genome_file;
+    string header_file;
 
     string outfile{"-"};
     const string description =
@@ -99,6 +100,8 @@ main_xcounts(int argc, const char **argv) {
                       false, genome_file);
     opt_parse.add_opt("reads", 'r', "ouput only sites with reads",
                       false, require_coverage);
+    opt_parse.add_opt("header", 'h', "use this file to generate header",
+                      false, header_file);
     opt_parse.add_opt("threads", 't', "threads for compression (use few)",
                       false, n_threads);
     std::vector<string> leftover_args;
@@ -150,7 +153,9 @@ main_xcounts(int argc, const char **argv) {
       tpool.set_io(out);
     }
 
-    if (!genome_file.empty())
+    if (!header_file.empty())
+      write_counts_header_from_file(header_file, out);
+    else if (!genome_file.empty())
       write_counts_header_from_chrom_sizes(chrom_names, chrom_sizes, out);
 
     // use the kstring_t type to more directly use the BGZF file
@@ -163,17 +168,20 @@ main_xcounts(int argc, const char **argv) {
     uint32_t offset = 0;
     string prev_chrom;
     bool status_ok = true;
+    bool found_header = (!genome_file.empty() || !header_file.empty());
 
     MSite site;
     while (status_ok && getline(in, line)) {
       if (is_counts_header_line(line.s)) {
-        if (!genome_file.empty()) continue;
+        if (!genome_file.empty() || !header_file.empty()) continue;
+        found_header = true;
         const string header_line{line.s};
         write_counts_header_line(header_line, out);
         continue;
       }
+
       status_ok = site.initialize(line.s, line.s + line.l);
-      if (!status_ok) break;
+      if (!status_ok || !found_header) break;
 
       if (site.chrom != prev_chrom) {
         prev_chrom = site.chrom;
@@ -196,6 +204,10 @@ main_xcounts(int argc, const char **argv) {
            << filename << " to " << outfile << endl;
       return EXIT_FAILURE;
     }
+    if (!found_header) {
+      cerr << "no header provided or found" << endl;
+      return EXIT_FAILURE;
+    }
   }
   catch (const std::exception &e) {
     cerr << e.what() << endl;