diff --git a/CHANGELOG.md b/CHANGELOG.md
index d68b0072..d1bb3e17 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608)
 - An option to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
 - Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/).
+- Haplocheck output files as input of MultiQC [#653]](https://github.com/nf-core/raredisease/pull/653)
 
 ### `Changed`
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 9f87335c..53538d6c 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -19,6 +19,7 @@ export_plots: true
 run_modules:
   - fastqc
   - fastp
+  - haplocheck
   - qualimap
   - picard
   - mosdepth
@@ -39,6 +40,8 @@ module_order:
       name: "fastp"
   - mosdepth:
       name: "Mosdepth"
+  - haplocheck:
+      name: "haplocheck"
   - ngsbits:
       name: "ngsbits"
   - peddy:
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index b606e17d..a43dd2fb 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -916,6 +916,7 @@ workflow RAREDISEASE {
     )
 
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(HAPLOCHECK.out.txt.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))