diff --git a/src/zen/fhir/generator.clj b/src/zen/fhir/generator.clj
index 5a545b7..96cae18 100644
--- a/src/zen/fhir/generator.clj
+++ b/src/zen/fhir/generator.clj
@@ -281,9 +281,22 @@
                (if (= inclusion-status :exclude)
                  (filter #(not= :bundled (:zen.fhir/content %)) nested-systems)
                  nested-systems))))
-         compose-elements)]
+         compose-elements)
+
+        code-systems-by-url
+        (group-by :fhir/url code-systems)]
     (into #{}
-          code-systems)))
+          (mapcat
+           (fn [[_url css-for-url]]
+             ;; Filter so that there is only one entry per URL
+             (let [unique-css (set css-for-url)]
+               (case (count unique-css)
+                 1 unique-css
+                 ;; When count is 2, CodeSystem comes as both :bundled and :not-present.
+                 ;; In this case only :not-present variant is kept
+                 ;; as :bundled implies that entire CodeSystem is present (i.e. it can’t be :not-bundled)
+                 2 (filter #(= :not-present (:zen.fhir/content %)) unique-css)))))
+          code-systems-by-url)))
 
 
 (defmethod generate-zen-schema :ValueSet [rt fhir-inter [url inter-res]]
diff --git a/test/zen/fhir/generator_test.clj b/test/zen/fhir/generator_test.clj
index 830dfcc..44da8db 100644
--- a/test/zen/fhir/generator_test.clj
+++ b/test/zen/fhir/generator_test.clj
@@ -28,9 +28,11 @@
       (def from-network-extension (-> "zen/fhir/plannet_fromnetwork_stripped.edn" io/resource slurp read-string))
       (def new-patients-extension (-> "zen/fhir/plannet_newpatients_stripped.edn" io/resource slurp read-string))
       (def practitioner-role-profile (-> "zen/fhir/plannet_practitionerrole_stripped.edn" io/resource slurp read-string))
+      (def multiple-same-url-includes-excludes-vs (-> "zen/fhir/ig-fiction_multiple-same-url-includes-excludes.edn" io/resource slurp read-string))
       (zen.fhir.core/load-definiton ztx {:url (:url practitioner-role-profile)} (assoc practitioner-role-profile :zen.fhir/package-ns "plannet"))
       (zen.fhir.core/load-definiton ztx {:url (:url new-patients-extension)} (assoc new-patients-extension :zen.fhir/package-ns "plannet"))
-      (zen.fhir.core/load-definiton ztx {:url (:url from-network-extension)} (assoc from-network-extension :zen.fhir/package-ns "plannet")))
+      (zen.fhir.core/load-definiton ztx {:url (:url from-network-extension)} (assoc from-network-extension :zen.fhir/package-ns "plannet"))
+      (zen.fhir.core/load-definiton ztx {:url (:url multiple-same-url-includes-excludes-vs)} (assoc multiple-same-url-includes-excludes-vs :zen.fhir/package-ns "ig-fiction")))
 
     (zen.fhir.core/load-all ztx nil
                             {:params {"hl7.fhir.r4.core" {:zen.fhir/package-ns 'fhir-r4}
@@ -408,7 +410,17 @@
                    :keys
                    {:dateTime  {:confirms #{'fhir-r4.dateTime/schema}, :fhir/flags #{:MS}},
                     :_dateTime {:confirms #{'fhir-r4.Element/schema}}},
-                   :require #{:dateTime}}}}}})
+                   :require #{:dateTime}}}}}
+
+     ;; Check that a CodeSystem present multiple times
+     ;; in compose.include and compose.exclude
+     ;; is not duplicated.
+     'ig-fiction.value-set.multiple-same-url-includes-excludes
+     {'value-set
+      {:zen/tags #{'zen.fhir/value-set}
+       :fhir/code-systems
+       #{{:fhir/url "http://example.com",
+          :zen.fhir/content :not-present}}}}})
 
   (t/testing "Intermediate representation is correct for"
     (t/testing "polymorphic keys defined on an element"
diff --git a/test/zen/fhir/ig-fiction_multiple-same-url-includes-excludes.edn b/test/zen/fhir/ig-fiction_multiple-same-url-includes-excludes.edn
new file mode 100644
index 0000000..23aabea
--- /dev/null
+++ b/test/zen/fhir/ig-fiction_multiple-same-url-includes-excludes.edn
@@ -0,0 +1,25 @@
+{:resourceType "ValueSet"
+ :id "multiple-same-url-includes-excludes"
+ :url "ig-fiction/multiple-same-url-includes-excludes"
+ :version "4.0.1"
+ :status "active"
+ :compose
+ {:include
+  [{:system "http://example.com"
+    :concept
+    [{:code "1"}
+     {:code "2"}
+     {:code "3"}]}
+   {:system "http://example.com"
+    :concept
+    [{:code "4"}
+     {:code "5"}]}
+   ;; Concepts for this element are not present on purpose
+   {:system "http://example.com"}]
+  :exclude
+  [{:system "http://example.com"
+    :concept
+    [{:code "6"}
+     {:code "7"}]}
+   ;; Concepts for this element are not present on purpose
+   {:system "http://example.com"}]}}