diff --git a/connectors/migrations/20230906_3_github_fill_parents_field.ts b/connectors/migrations/20230906_3_github_fill_parents_field.ts
new file mode 100644
index 000000000000..df42b9f210de
--- /dev/null
+++ b/connectors/migrations/20230906_3_github_fill_parents_field.ts
@@ -0,0 +1,104 @@
+import {
+  getDiscussionDocumentId,
+  getIssueDocumentId,
+} from "@connectors/connectors/github/temporal/activities";
+import { updateDocumentParentsField } from "@connectors/lib/data_sources";
+import {
+  Connector,
+  GithubDiscussion,
+  GithubIssue,
+} from "@connectors/lib/models";
+
+async function main() {
+  if (!process.argv[2]) {
+    console.error("Missing workspace id or 'all' as first argument");
+    process.exit(1);
+  }
+  // if first arg is "all", update all connectors, else update only the
+  // connector for the corresponding workspace id
+  const connectors =
+    process.argv[2] === "all"
+      ? await Connector.findAll({
+          where: {
+            type: "github",
+          },
+        })
+      : await Connector.findAll({
+          where: {
+            type: "github",
+            workspaceId: process.argv[2],
+          },
+        });
+
+  for (const connector of connectors) {
+    console.log(`Updating parents field for connector ${connector.id}`);
+    await updateDiscussionsParentsFieldForConnector(connector);
+    await updateIssuesParentsFieldForConnector(connector);
+  }
+}
+
+async function updateDiscussionsParentsFieldForConnector(connector: Connector) {
+  // get all distinct documentIds and their channel ids from slack messages in
+  // this connector
+  const documentData = await GithubDiscussion.findAll({
+    where: {
+      connectorId: connector.id,
+    },
+    attributes: ["repoId", "discussionNumber"],
+  });
+  // update all parents fields for discussions by chunks of 128
+  const chunkSize = 32;
+  for (let i = 0; i < documentData.length; i += chunkSize) {
+    const chunk = documentData.slice(i, i + chunkSize);
+    console.log(`Updating ${chunk.length} documents`);
+    // update parents field for each document of the chunk, in parallel
+    await Promise.all(
+      chunk.map(async (document) => {
+        const docId = getDiscussionDocumentId(
+          document.repoId,
+          document.discussionNumber
+        );
+        await updateDocumentParentsField(connector, docId, [
+          getDiscussionDocumentId(document.repoId, document.discussionNumber),
+          document.repoId,
+        ]);
+      })
+    );
+  }
+}
+
+async function updateIssuesParentsFieldForConnector(connector: Connector) {
+  // get all distinct issues  and their repo ids fro
+  const documentData = await GithubIssue.findAll({
+    where: {
+      connectorId: connector.id,
+    },
+    attributes: ["repoId", "issueNumber"],
+  });
+  // update all parents fields for all issues by chunks of 128
+  const chunkSize = 32;
+  for (let i = 0; i < documentData.length; i += chunkSize) {
+    const chunk = documentData.slice(i, i + chunkSize);
+    console.log(`Updating ${chunk.length} documents`);
+    // update parents field for each document of the chunk, in parallel
+    await Promise.all(
+      chunk.map(async (document) => {
+        const docId = getIssueDocumentId(document.repoId, document.issueNumber);
+        await updateDocumentParentsField(connector, docId, [
+          getIssueDocumentId(document.repoId, document.issueNumber),
+          document.repoId,
+        ]);
+      })
+    );
+  }
+}
+
+main()
+  .then(() => {
+    console.log("Done");
+    process.exit(0);
+  })
+  .catch((err) => {
+    console.error(err);
+    process.exit(1);
+  });
diff --git a/connectors/src/connectors/github/temporal/activities.ts b/connectors/src/connectors/github/temporal/activities.ts
index 6fc6295f3c2c..c97c7723eb24 100644
--- a/connectors/src/connectors/github/temporal/activities.ts
+++ b/connectors/src/connectors/github/temporal/activities.ts
@@ -154,7 +154,16 @@ export async function githubUpsertIssueActivity(
     documentUrl: issue.url,
     timestampMs: lastUpdateTimestamp,
     tags: tags,
-    parents: [],
+    // The convention for parents is to use the external id string; it is ok for
+    // repos, but not practical for issues since the external id is the
+    // issue number, which is not guaranteed unique in the workspace.
+    // Therefore as a special case we use getIssueDocumentId() to get a parent string
+    // The repo id from github is globally unique so used as-is, as per
+    // convention to use the external id string.
+    parents: [
+      getIssueDocumentId(repoId.toString(), issue.number),
+      repoId.toString(),
+    ],
     retries: 3,
     delayBetweenRetriesMs: 500,
     loggerArgs: { ...loggerArgs, provider: "github" },
@@ -281,7 +290,16 @@ export async function githubUpsertDiscussionActivity(
     documentUrl: discussion.url,
     timestampMs: new Date(discussion.createdAt).getTime(),
     tags,
-    parents: [],
+    // The convention for parents is to use the external id string; it is ok for
+    // repos, but not practical for discussions since the external id is the
+    // issue number, which is not guaranteed unique in the workspace. Therefore
+    // as a special case we use getDiscussionDocumentId() to get a parent string
+    // The repo id from github is globally unique so used as-is, as per
+    // convention to use the external id string.
+    parents: [
+      getDiscussionDocumentId(repoId.toString(), discussionNumber),
+      repoId.toString(),
+    ],
     retries: 3,
     delayBetweenRetriesMs: 500,
     loggerArgs: { ...loggerArgs, provider: "github" },
@@ -585,11 +603,14 @@ function renderGithubUser(user: GithubUser | null): string {
   return `@${user.id}`;
 }
 
-function getIssueDocumentId(repoId: string, issueNumber: number): string {
+export function getIssueDocumentId(
+  repoId: string,
+  issueNumber: number
+): string {
   return `github-issue-${repoId}-${issueNumber}`;
 }
 
-function getDiscussionDocumentId(
+export function getDiscussionDocumentId(
   repoId: string,
   discussionNumber: number
 ): string {
diff --git a/connectors/src/types/resources.ts b/connectors/src/types/resources.ts
index 47f7b7e47d9d..f4d8771f335d 100644
--- a/connectors/src/types/resources.ts
+++ b/connectors/src/types/resources.ts
@@ -15,8 +15,19 @@ export type ConnectorResourceType = "file" | "folder" | "database" | "channel";
  * - Slack: channels
  * - GoogleDrive: shared drive or sub-folders of shared drives.
  *
- * `internalId` and `parentInternalId` are internal opaque identifiers that should enable
- * reconstructing the tree structure of the resources.
+ * `internalId` and `parentInternalId` are internal opaque identifiers that
+ * should enable reconstructing the tree structure of the resources.
+ *
+ * Those ids must be aligned with those used in the "parents" field of data
+ * sources documents, to enable search filter on documents based on their
+ * parents, see the
+ *
+ * The convention to use for internal ids are to always use the externally
+ * provided id when possible (e.g. Notion page id, Github repository id,
+ * etc...). When not possible, such as for Github issues whose id is not
+ * workspace-unique, a custom function to create a unique id is created, and
+ * used both in the parents field management code and the connectors resource
+ * code.
  */
 export type ConnectorResource = {
   provider: ConnectorProvider;
diff --git a/core/src/data_sources/data_source.rs b/core/src/data_sources/data_source.rs
index 3f0ad1338d48..388c1230f050 100644
--- a/core/src/data_sources/data_source.rs
+++ b/core/src/data_sources/data_source.rs
@@ -95,19 +95,25 @@ pub struct Chunk {
 /// The "parents" field is an array of ids of parents to the document,
 /// corresponding to its hierarchy, ordered by closest parent first.
 ///
-/// At index 0 is the document id itself, then at index 1 its direct parent,
-/// then at index 2 is the direct parent of the element represented at index 1,
-/// etc. It is assumed that a document (or folder, or hierarchical level) only
-/// has at most one direct parent. Therefore, there is an unambiguous mapping
-/// between the parents array and the document's hierarchical position. For
-/// example, for a regular file system (or filesystem-like such as Google
-/// Drive), each parent would correspond to a subfolder in the path to the
-/// document.
+/// Parents are at the time of writing only relevant for managed datasources
+/// since standard datasources do not allow specifying a hierarchy. A parent is
+/// represented by a string of characters which correspond to the parent's
+/// external id, provided by the managed datasource’s API (e.g. the Notion id
+/// for Notion pages and databases).
+///
+/// At index 0 is the string id of the document itself, then at index 1 its
+/// direct parent, then at index 2 is the direct parent of the element
+/// represented at index 1, etc. It is assumed that a document (or folder, or
+/// hierarchical level) only has at most one direct parent. Therefore, there is
+/// an unambiguous mapping between the parents array and the document's
+/// hierarchical position. For example, for a regular file system (or
+/// filesystem-like such as Google Drive), each parent would correspond to a
+/// subfolder in the path to the document.
 ///
-/// The document’s id is stored in the field, since the field is used in
-/// filtering search to search only parts of the hierarchy: it is natural that
-/// if the document’s id is selected as a parent filter, the document itself
-/// shows up in the search.
+/// The id of the document itself is stored at index 0 because the field is used
+/// in filtering search to search only parts of the hierarchy: it is natural
+/// that if the document’s id is selected as a parent filter, the document
+/// itself shows up in the search.
 ///
 ///
 /// Note however that the hierarchical system depends on the managed datasource.
@@ -116,11 +122,9 @@ pub struct Chunk {
 /// no slack ids for our slack "documents" so the only value in the parents
 /// array is the slack channel id
 ///
-/// Parents are at the time of writing only relevant for managed datasources
-/// since standard datasources do not allow specifying a hierarchy. A parent is
-/// represented by a string of characters which correspond to the parent's
-/// internal id (specific to the managed datasource)--not its name--provided by
-/// the managed datasource.
+/// For github, github issues / discussions do not have a proper external id, so
+/// we use our computed document id. The repo is considered a parent, and has a
+/// proper external “repo id”, which is stored at 2nd place in the array
 
 #[derive(Debug, Serialize, Clone)]
 pub struct Document {