diff --git a/openfpga/src/annotation/annotate_pb_graph.cpp b/openfpga/src/annotation/annotate_pb_graph.cpp
index 92f1b90b2..d720426cc 100644
--- a/openfpga/src/annotation/annotate_pb_graph.cpp
+++ b/openfpga/src/annotation/annotate_pb_graph.cpp
@@ -10,6 +10,7 @@
 #include "pb_graph_utils.h"
 
 #include "annotate_pb_graph.h"
+#include "check_pb_graph_annotation.h"
 
 /* begin namespace openfpga */
 namespace openfpga {
@@ -435,6 +436,9 @@ void annotate_pb_graph(const DeviceContext& vpr_device_ctx,
   VTR_LOG("Binding operating pb_graph nodes/pins to physical pb_graph nodes/pins...\n");
   annotate_physical_pb_graph_node(vpr_device_ctx, vpr_pb_type_annotation);
   VTR_LOG("Done\n");
+
+  /* Check each primitive pb_graph_node and pin has been binded to a physical node and pin */
+  check_physical_pb_graph_node_annotation(vpr_device_ctx, const_cast<const VprPbTypeAnnotation&>(vpr_pb_type_annotation));
 }
 
 } /* end namespace openfpga */
diff --git a/openfpga/src/annotation/check_pb_graph_annotation.cpp b/openfpga/src/annotation/check_pb_graph_annotation.cpp
new file mode 100644
index 000000000..92cabefb4
--- /dev/null
+++ b/openfpga/src/annotation/check_pb_graph_annotation.cpp
@@ -0,0 +1,124 @@
+/********************************************************************
+ * This file includes functions to check the  annotation on
+ * the physical pb_graph_node and pb_graph_pin
+ *******************************************************************/
+/* Headers from vtrutil library */
+#include "vtr_time.h"
+#include "vtr_assert.h"
+#include "vtr_log.h"
+
+#include "pb_type_utils.h"
+#include "check_pb_graph_annotation.h"
+
+/* begin namespace openfpga */
+namespace openfpga {
+
+/********************************************************************
+ * A function to check if a physical pb_graph_pin for a pb_graph_pin 
+ * Print error to log file/screen when checking fails
+ *******************************************************************/
+static 
+bool check_physical_pb_graph_pin(t_pb_graph_pin* pb_graph_pin,
+                                 const VprPbTypeAnnotation& vpr_pb_type_annotation) {
+  if (nullptr == vpr_pb_type_annotation.physical_pb_graph_pin(pb_graph_pin)) {
+    VTR_LOG_ERROR("Found a pb_graph_pin '%s' missing physical pb_graph_pin binding!\n",
+                  pb_graph_pin->port->name);
+    return false;
+  }
+
+  return true;
+}
+
+/********************************************************************
+ * This function will recursively walk through all the pb_graph nodes
+ * starting from a top node.
+ * It aims to check 
+ * - if each primitive pb_graph node has been binded to a physical 
+ *   pb_graph_node
+ * - if each pin of the primitive pb_graph node has been binded to 
+ *   a physical graph_pin
+ *******************************************************************/
+static 
+void rec_check_vpr_physical_pb_graph_node_annotation(t_pb_graph_node* pb_graph_node, 
+                                                     const VprPbTypeAnnotation& vpr_pb_type_annotation,
+                                                     size_t& num_err) {
+  /* Go recursive first until we touch the primitive node */
+  if (false == is_primitive_pb_type(pb_graph_node->pb_type)) {
+    for (int imode = 0; imode < pb_graph_node->pb_type->num_modes; ++imode) {
+      for (int ipb = 0; ipb < pb_graph_node->pb_type->modes[imode].num_pb_type_children; ++ipb) {
+        /* Each child may exist multiple times in the hierarchy*/
+        for (int jpb = 0; jpb < pb_graph_node->pb_type->modes[imode].pb_type_children[ipb].num_pb; ++jpb) {
+          rec_check_vpr_physical_pb_graph_node_annotation(&(pb_graph_node->child_pb_graph_nodes[imode][ipb][jpb]), 
+                                                          vpr_pb_type_annotation, num_err);
+        }
+      }
+    }
+    return;
+  }
+
+  /* Ensure that the pb_graph_node has been mapped to a physical node */
+  t_pb_graph_node* physical_pb_graph_node = vpr_pb_type_annotation.physical_pb_graph_node(pb_graph_node);
+  if (nullptr == physical_pb_graph_node) { 
+    VTR_LOG_ERROR("Found a pb_graph_node '%s' missing physical pb_graph_node binding!\n",
+                  physical_pb_graph_node->pb_type->name);
+    num_err++;
+    return; /* Invalid pointer already, further check is not applicable */
+  } 
+
+  /* Reach here, we should have a valid pointer to the physical pb_graph_node,
+   * Check the physical pb_graph_pin for each pin 
+   */
+  for (int iport = 0; iport < physical_pb_graph_node->num_input_ports; ++iport) {
+    for (int ipin = 0; ipin < physical_pb_graph_node->num_input_pins[iport]; ++ipin) {
+      if (false == check_physical_pb_graph_pin(&(physical_pb_graph_node->input_pins[iport][ipin]),
+                                               vpr_pb_type_annotation)) {
+        num_err++;
+      }
+    } 
+  }
+
+  for (int iport = 0; iport < physical_pb_graph_node->num_output_ports; ++iport) {
+    for (int ipin = 0; ipin < physical_pb_graph_node->num_output_pins[iport]; ++ipin) {
+      if (false == check_physical_pb_graph_pin(&(physical_pb_graph_node->output_pins[iport][ipin]),
+                                               vpr_pb_type_annotation)) {
+        num_err++;
+      }
+    } 
+  }
+
+  for (int iport = 0; iport < physical_pb_graph_node->num_clock_ports; ++iport) {
+    for (int ipin = 0; ipin < physical_pb_graph_node->num_clock_pins[iport]; ++ipin) {
+      if (false == check_physical_pb_graph_pin(&(physical_pb_graph_node->clock_pins[iport][ipin]),
+                                               vpr_pb_type_annotation)) {
+        num_err++;
+      }
+    } 
+  }
+}
+
+/********************************************************************
+ * Check each primitive pb_graph_node
+ * - It has been binded to an physical pb_graph_node
+ * - Each pin has been binded to a physical pb_graph_node pin
+ *******************************************************************/
+void check_physical_pb_graph_node_annotation(const DeviceContext& vpr_device_ctx, 
+                                             const VprPbTypeAnnotation& vpr_pb_type_annotation) {
+  size_t num_err = 0;
+ 
+  for (const t_logical_block_type& lb_type : vpr_device_ctx.logical_block_types) {
+    /* By pass nullptr for pb_graph head */
+    if (nullptr == lb_type.pb_graph_head) {
+      continue;
+    }
+    rec_check_vpr_physical_pb_graph_node_annotation(lb_type.pb_graph_head, vpr_pb_type_annotation, num_err); 
+  }
+
+  if (0 == num_err) {
+    VTR_LOG("Check pb_graph annotation for physical nodes and pins passed.\n");
+  } else {
+    VTR_LOG_ERROR("Check pb_graph annotation for physical nodes and pins failed with %ld errors!\n",
+                  num_err);
+  }
+}
+
+} /* end namespace openfpga */
diff --git a/openfpga/src/annotation/check_pb_graph_annotation.h b/openfpga/src/annotation/check_pb_graph_annotation.h
new file mode 100644
index 000000000..c482943c5
--- /dev/null
+++ b/openfpga/src/annotation/check_pb_graph_annotation.h
@@ -0,0 +1,23 @@
+#ifndef CHECK_PB_GRAPH_ANNOTATION_H
+#define CHECK_PB_GRAPH_ANNOTATION_H
+
+/********************************************************************
+ * Include header files that are required by function declaration
+ *******************************************************************/
+#include "vpr_context.h"
+#include "openfpga_context.h"
+#include "vpr_pb_type_annotation.h"
+
+/********************************************************************
+ * Function declaration
+ *******************************************************************/
+
+/* begin namespace openfpga */
+namespace openfpga {
+
+void check_physical_pb_graph_node_annotation(const DeviceContext& vpr_device_ctx, 
+                                             const VprPbTypeAnnotation& vpr_pb_type_annotation);
+
+} /* end namespace openfpga */
+
+#endif