diff --git a/erpnext/manufacturing/doctype/bom/bom.py b/erpnext/manufacturing/doctype/bom/bom.py
index b470f5bbfe..f6cdb2e57c 100644
--- a/erpnext/manufacturing/doctype/bom/bom.py
+++ b/erpnext/manufacturing/doctype/bom/bom.py
@@ -835,6 +835,10 @@ def add_operations_cost(stock_entry, work_order=None, expense_account=None):
 def get_bom_diff(bom1, bom2):
 	from frappe.model import table_fields
 
+	if bom1 == bom2:
+		frappe.throw(_("BOM 1 {0} and BOM 2 {1} should not be same")
+			.format(frappe.bold(bom1), frappe.bold(bom2)))
+
 	doc1 = frappe.get_doc('BOM', bom1)
 	doc2 = frappe.get_doc('BOM', bom2)
 
diff --git a/erpnext/manufacturing/page/bom_comparison_tool/bom_comparison_tool.js b/erpnext/manufacturing/page/bom_comparison_tool/bom_comparison_tool.js
index 7152d3dff6..1bcb1efdaa 100644
--- a/erpnext/manufacturing/page/bom_comparison_tool/bom_comparison_tool.js
+++ b/erpnext/manufacturing/page/bom_comparison_tool/bom_comparison_tool.js
@@ -22,7 +22,14 @@ erpnext.BOMComparisonTool = class BOMComparisonTool {
 					fieldname: 'name1',
 					fieldtype: 'Link',
 					options: 'BOM',
-					change: () => this.fetch_and_render()
+					change: () => this.fetch_and_render(),
+					get_query: () => {
+						return {
+							filters: {
+								"name": ["not in", [this.form.get_value("name2") || ""]]
+							}
+						}
+					}
 				},
 				{
 					fieldtype: 'Column Break'
@@ -32,7 +39,14 @@ erpnext.BOMComparisonTool = class BOMComparisonTool {
 					fieldname: 'name2',
 					fieldtype: 'Link',
 					options: 'BOM',
-					change: () => this.fetch_and_render()
+					change: () => this.fetch_and_render(),
+					get_query: () => {
+						return {
+							filters: {
+								"name": ["not in", [this.form.get_value("name1") || ""]]
+							}
+						}
+					}
 				},
 				{
 					fieldtype: 'Section Break'