diff --git a/src/glsl/linker.cpp b/src/glsl/linker.cpp
index 330fae004b3..52a277eb719 100644
--- a/src/glsl/linker.cpp
+++ b/src/glsl/linker.cpp
@@ -2558,6 +2558,7 @@ add_interface_variables(struct gl_shader_program *shProg,
 {
    foreach_in_list(ir_instruction, node, sh->ir) {
       ir_variable *var = node->as_variable();
+      uint8_t mask = 0;
 
       if (!var)
          continue;
@@ -2573,6 +2574,10 @@ add_interface_variables(struct gl_shader_program *shProg,
              var->data.location != SYSTEM_VALUE_VERTEX_ID_ZERO_BASE &&
              var->data.location != SYSTEM_VALUE_INSTANCE_ID)
             continue;
+         /* Mark special built-in inputs referenced by the vertex stage so
+          * that they are considered active by the shader queries.
+          */
+         mask = (1 << (MESA_SHADER_VERTEX));
          /* FALLTHROUGH */
       case ir_var_shader_in:
          if (programInterface != GL_PROGRAM_INPUT)
@@ -2587,7 +2592,7 @@ add_interface_variables(struct gl_shader_program *shProg,
       };
 
       if (!add_program_resource(shProg, programInterface, var,
-                                build_stageref(shProg, var->name)))
+                                build_stageref(shProg, var->name) | mask))
          return false;
    }
    return true;